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 28692,SRR26535343,SRX22238470,SRS19292731,SRP468564,PRJNA1032461,A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo,GSE246295,Transcriptome Analysis,To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 alongside three control brains from injected siblings who did not develop tumors CTRL 1 3 were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.,,pubmed:39052000,,EGFRviii PI3KCAH1047R mScarlet tumor negative control brain 2,GSM7866394,,source name:Whole Brain|strain:CG1 p53null|tissue:Whole Brain|geo loc name:missing|collection date:missing,EGFRviii PI3KCAH1047R mScarlet tumor negative control brain 2,Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A “decoy aware” index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions.,Whole Brain,Fertilized embryos injected with either EPS or KPG construct mix,Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer’s recommendations,Zebrafish were housed and reared following approved animal use protocol,strain:CG1 p53null|tissue:Whole Brain,GSM7866394,GSM7866394: EGFRviii PI3KCAH1047R mScarlet tumor negative control brain 2; Danio rerio; RNA Seq,GSM7866394 r1,GSM7866394,1,Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP468564,,loader:fastq load.py,CTRL_3.fastq.gz,fastq,7081948098.0,70118298.0,GSM7866394 r1,0:101,A:1894557984;C:1627945034;G:1550203852;T:2009224463;N:16765,101,,,,1894557984,1627945034,1550203852,2009224463,16765,SRX22238470,SRS19292731,SRA1740017,"Hayes Lab, DSCB, Sickkids Research","Hayes Lab, DSCB, Sickkids Research",1,0.94543,,0.14646,,0.68883,,0.49451,,101,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Canada,2023-10-26,Undetermined,Embryo,Brain,Nervous System 28693,SRR26535344,SRX22238469,SRS19292730,SRP468564,PRJNA1032461,A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo,GSE246295,Transcriptome Analysis,To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 alongside three control brains from injected siblings who did not develop tumors CTRL 1 3 were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.,,pubmed:39052000,,EGFRviii PI3KCAH1047R mScarlet tumor negative control brain 1,GSM7866393,,source name:Whole Brain|strain:CG1 p53null|tissue:Whole Brain|geo loc name:missing|collection date:missing,EGFRviii PI3KCAH1047R mScarlet tumor negative control brain 1,Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A “decoy aware” index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions.,Whole Brain,Fertilized embryos injected with either EPS or KPG construct mix,Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer’s recommendations,Zebrafish were housed and reared following approved animal use protocol,strain:CG1 p53null|tissue:Whole Brain,GSM7866393,GSM7866393: EGFRviii PI3KCAH1047R mScarlet tumor negative control brain 1; Danio rerio; RNA Seq,GSM7866393 r1,GSM7866393,1,Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP468564,,loader:fastq load.py,CTRL_2.fastq.gz,fastq,7840572329.0,77629429.0,GSM7866393 r1,0:101,A:2099360211;C:1783653297;G:1717681461;T:2239858766;N:18594,101,,,,2099360211,1783653297,1717681461,2239858766,18594,SRX22238469,SRS19292730,SRA1740017,"Hayes Lab, DSCB, Sickkids Research","Hayes Lab, DSCB, Sickkids Research",1,0.93984,,0.1663,,0.69033,,0.484,,101,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Canada,2023-10-26,Undetermined,Embryo,Brain,Nervous System 28694,SRR26535345,SRX22238468,SRS19292729,SRP468564,PRJNA1032461,A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo,GSE246295,Transcriptome Analysis,To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 alongside three control brains from injected siblings who did not develop tumors CTRL 1 3 were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.,,pubmed:39052000,,KRAS PI3KCAH1047R GFP tumor negative control brain,GSM7866392,,source name:Whole Brain|strain:CG1 p53null|tissue:Whole Brain|geo loc name:missing|collection date:missing,KRAS PI3KCAH1047R GFP tumor negative control brain,Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A “decoy aware” index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions.,Whole Brain,Fertilized embryos injected with either EPS or KPG construct mix,Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer’s recommendations,Zebrafish were housed and reared following approved animal use protocol,strain:CG1 p53null|tissue:Whole Brain,GSM7866392,GSM7866392: KRAS PI3KCAH1047R GFP tumor negative control brain; Danio rerio; RNA Seq,GSM7866392 r1,GSM7866392,1,Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP468564,,loader:fastq load.py,CTRL_1.fastq.gz,fastq,10164914720.0,100642720.0,GSM7866392 r1,0:101,A:2650336113;C:2354113843;G:2276252979;T:2884188285;N:23500,101,,,,2650336113,2354113843,2276252979,2884188285,23500,SRX22238468,SRS19292729,SRA1740017,"Hayes Lab, DSCB, Sickkids Research","Hayes Lab, DSCB, Sickkids Research",1,0.94271,,0.10831,,0.68527,,0.50207,,101,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Canada,2023-10-26,Undetermined,Embryo,Brain,Nervous System 28695,SRR26535346,SRX22238467,SRS19292728,SRP468564,PRJNA1032461,A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo,GSE246295,Transcriptome Analysis,To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 alongside three control brains from injected siblings who did not develop tumors CTRL 1 3 were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.,,pubmed:39052000,,EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 3,GSM7866391,,source name:Whole Brain|strain:CG1 p53null|tissue:Whole Brain|geo loc name:missing|collection date:missing,EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 3,Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A “decoy aware” index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions.,Whole Brain,Fertilized embryos injected with either EPS or KPG construct mix,Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer’s recommendations,Zebrafish were housed and reared following approved animal use protocol,strain:CG1 p53null|tissue:Whole Brain,GSM7866391,GSM7866391: EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 3; Danio rerio; RNA Seq,GSM7866391 r1,GSM7866391,1,Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP468564,,loader:fastq load.py,EPS_3.fastq.gz,fastq,9796714170.0,96997170.0,GSM7866391 r1,0:101,A:2627522717;C:2223655583;G:2134761894;T:2810751194;N:22782,101,,,,2627522717,2223655583,2134761894,2810751194,22782,SRX22238467,SRS19292728,SRA1740017,"Hayes Lab, DSCB, Sickkids Research","Hayes Lab, DSCB, Sickkids Research",1,0.92543,,0.1876,,0.67308,,0.4886,,101,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Canada,2023-10-26,Undetermined,Embryo,Brain,Nervous System 28696,SRR26535347,SRX22238466,SRS19292727,SRP468564,PRJNA1032461,A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo,GSE246295,Transcriptome Analysis,To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 alongside three control brains from injected siblings who did not develop tumors CTRL 1 3 were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.,,pubmed:39052000,,EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 2,GSM7866390,,source name:Whole Brain|strain:CG1 p53null|tissue:Whole Brain|geo loc name:missing|collection date:missing,EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 2,Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A “decoy aware” index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions.,Whole Brain,Fertilized embryos injected with either EPS or KPG construct mix,Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer’s recommendations,Zebrafish were housed and reared following approved animal use protocol,strain:CG1 p53null|tissue:Whole Brain,GSM7866390,GSM7866390: EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 2; Danio rerio; RNA Seq,GSM7866390 r1,GSM7866390,1,Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP468564,,loader:fastq load.py,EPS_2.fastq.gz,fastq,7839595861.0,77619761.0,GSM7866390 r1,0:101,A:2093456023;C:1792947580;G:1718784421;T:2234389453;N:18384,101,,,,2093456023,1792947580,1718784421,2234389453,18384,SRX22238466,SRS19292727,SRA1740017,"Hayes Lab, DSCB, Sickkids Research","Hayes Lab, DSCB, Sickkids Research",1,0.93807,,0.14978,,0.68854,,0.47786,,101,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Canada,2023-10-26,Undetermined,Embryo,Brain,Nervous System 28697,SRR26535348,SRX22238465,SRS19292726,SRP468564,PRJNA1032461,A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo,GSE246295,Transcriptome Analysis,To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 alongside three control brains from injected siblings who did not develop tumors CTRL 1 3 were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.,,pubmed:39052000,,EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 1,GSM7866389,,source name:Whole Brain|strain:CG1 p53null|tissue:Whole Brain|geo loc name:missing|collection date:missing,EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 1,Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A “decoy aware” index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions.,Whole Brain,Fertilized embryos injected with either EPS or KPG construct mix,Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer’s recommendations,Zebrafish were housed and reared following approved animal use protocol,strain:CG1 p53null|tissue:Whole Brain,GSM7866389,GSM7866389: EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 1; Danio rerio; RNA Seq,GSM7866389 r1,GSM7866389,1,Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP468564,,loader:fastq load.py,EPS_1.fastq.gz,fastq,8403475528.0,83202728.0,GSM7866389 r1,0:101,A:2217465507;C:1940028683;G:1857031218;T:2388930530;N:19590,101,,,,2217465507,1940028683,1857031218,2388930530,19590,SRX22238465,SRS19292726,SRA1740017,"Hayes Lab, DSCB, Sickkids Research","Hayes Lab, DSCB, Sickkids Research",1,0.94596,,0.12916,,0.68619,,0.4957,,101,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Canada,2023-10-26,Undetermined,Embryo,Brain,Nervous System 28698,SRR26535349,SRX22238464,SRS19292725,SRP468564,PRJNA1032461,A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo,GSE246295,Transcriptome Analysis,To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 alongside three control brains from injected siblings who did not develop tumors CTRL 1 3 were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.,,pubmed:39052000,,KRAS PI3KCAH1047R GFP tumor positive whole brain 3,GSM7866388,,source name:Whole Brain|strain:CG1 p53null|tissue:Whole Brain|geo loc name:missing|collection date:missing,KRAS PI3KCAH1047R GFP tumor positive whole brain 3,Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A “decoy aware” index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions.,Whole Brain,Fertilized embryos injected with either EPS or KPG construct mix,Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer’s recommendations,Zebrafish were housed and reared following approved animal use protocol,strain:CG1 p53null|tissue:Whole Brain,GSM7866388,GSM7866388: KRAS PI3KCAH1047R GFP tumor positive whole brain 3; Danio rerio; RNA Seq,GSM7866388 r1,GSM7866388,1,Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP468564,,loader:fastq load.py,KPG_3.fastq.gz,fastq,7609183450.0,75338450.0,GSM7866388 r1,0:101,A:2040241047;C:1721563382;G:1666400346;T:2180961056;N:17619,101,,,,2040241047,1721563382,1666400346,2180961056,17619,SRX22238464,SRS19292725,SRA1740017,"Hayes Lab, DSCB, Sickkids Research","Hayes Lab, DSCB, Sickkids Research",1,0.93555,,0.16895,,0.68199,,0.50032,,101,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Canada,2023-10-26,Undetermined,Embryo,Brain,Nervous System 28699,SRR26535350,SRX22238463,SRS19292724,SRP468564,PRJNA1032461,A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo,GSE246295,Transcriptome Analysis,To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 alongside three control brains from injected siblings who did not develop tumors CTRL 1 3 were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.,,pubmed:39052000,,KRAS PI3KCAH1047R GFP tumor positive whole brain 2,GSM7866387,,source name:Whole Brain|strain:CG1 p53null|tissue:Whole Brain|geo loc name:missing|collection date:missing,KRAS PI3KCAH1047R GFP tumor positive whole brain 2,Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A “decoy aware” index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions.,Whole Brain,Fertilized embryos injected with either EPS or KPG construct mix,Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer’s recommendations,Zebrafish were housed and reared following approved animal use protocol,strain:CG1 p53null|tissue:Whole Brain,GSM7866387,GSM7866387: KRAS PI3KCAH1047R GFP tumor positive whole brain 2; Danio rerio; RNA Seq,GSM7866387 r1,GSM7866387,1,Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP468564,,loader:fastq load.py,KPG_2.fastq.gz,fastq,8446573339.0,83629439.0,GSM7866387 r1,0:101,A:2223763293;C:1944013929;G:1869828652;T:2408947564;N:19901,101,,,,2223763293,1944013929,1869828652,2408947564,19901,SRX22238463,SRS19292724,SRA1740017,"Hayes Lab, DSCB, Sickkids Research","Hayes Lab, DSCB, Sickkids Research",1,0.94943,,0.11539,,0.68428,,0.51019,,101,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Canada,2023-10-26,Undetermined,Embryo,Brain,Nervous System 28700,SRR26535351,SRX22238462,SRS19292723,SRP468564,PRJNA1032461,A syngeneic spontaneous zebrafish model oftp53 deficient EGFRviii and PI3KCAH1047R driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapsein vivo,GSE246295,Transcriptome Analysis,To build a patient relevantin vivomodel of human glioblastoma we expressed common oncogenic variants including activated human EGFRviii or KRAS and PI3KCAH1047Runder the control of the radial glial specific promoterher4.1in syngeneictp53loss of function mutant zebrafish.Robust tumor formation was observed prior to 45 days of life with a gene expression signature similar to human glioblastoma of the mesenchymal subtype along with a strong inflammatory component. Within early stage tumor lesions and in an intact and endogenous tumor microenvironment we visualized infiltration of phagocytic cells as well as internalization of tumor cells bympeg1.1:GFP+ microglia/macrophages suggesting negative regulatory pressure by pro inflammatory cell types on tumor growth at early stages of glioblastoma initiationin vivo. Furthermore CRISPR/Cas9 mediated gene targeting of master inflammatory transcription factorsirf7andirf8led to increased tumor formation in the primary context while suppression of microglial/macrophage activity led to enhanced tumor cell engraftment following transplantation into otherwise immune competent zebrafish hosts. Altogether we developed a genetically relevant model of aggressive human glioblastoma and harnessed the unique advantages of zebrafish including live imaging high throughput genetic and chemical manipulations to highlight important tumor suppressive roles for the innate immune system on glioblastoma initiation with important future significance for therapeutic discovery and optimizations. Overall design: To capture broad transcriptomic differences in tumor burdened brains versus normal brains we performed bulk RNA sequencing and gene expression analysis of whole brains and sorted cells. EGFRviii derived tumors were induced by microinjection of EGFRviii PI3KCAH1047R and mScarlet constructs defined as EPS. KRAS derived tumors were induced by microinjection of KRAS PI3KCAH1047R GFP constructs defined as KPG. Three whole brains positive for fluorescent tumors EPS 1 3 KPG 1 3 alongside three control brains from injected siblings who did not develop tumors CTRL 1 3 were dissected for each condition for bulk RNA sequencing. We also performed fluorescent activated cell sorting on pooled dissociated brains from the EPS condition resulting in enrichment for mScarlet postive tumor cells CS Pos and mScarlet negative cells CS Neg for comparative analysis.,,pubmed:39052000,,KRAS PI3KCAH1047R GFP tumor positive whole brain 1,GSM7866386,,source name:Whole Brain|strain:CG1 p53null|tissue:Whole Brain|geo loc name:missing|collection date:missing,KRAS PI3KCAH1047R GFP tumor positive whole brain 1,Raw .fastq data was processed using Salmon quantification of transcripts for each sample. A “decoy aware” index was built with the Danio rerio transcriptome and genome using the GRCz11 assembly with a k mers length of 23 with entries manually added for GFP mScarlet EGFRviii KRAS and PI3KCAH1047R transcripts. Samples were then quantified with the following arguments: r seqBias mp 3 validateMappings rangeFactorizationBins 4. Differential gene expression was compared utilizing DESeq2 and GSEA. Assembly: GRCz11 Supplementary files format and content: Tab delimited .csv file including raw counts for all conditions.,Whole Brain,Fertilized embryos injected with either EPS or KPG construct mix,Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer’s recommendations,Zebrafish were housed and reared following approved animal use protocol,strain:CG1 p53null|tissue:Whole Brain,GSM7866386,GSM7866386: KRAS PI3KCAH1047R GFP tumor positive whole brain 1; Danio rerio; RNA Seq,GSM7866386 r1,GSM7866386,1,Dissected brains or sorted cells were immediately put into Trizol. RNA was then extracted and purified utilizing Monarch RNA Cleanup Kit following manufacturer's recommendations Sequence ready polyA enriched libraries were prepared using the NEB Ultra II Directional mRNA prep kit for Illumina according to manufacturer's recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP468564,,loader:fastq load.py,KPG_1.fastq.gz,fastq,4326209053.0,42833753.0,GSM7866386 r1,0:101,A:1143856405;C:993993009;G:951829931;T:1236519669;N:10039,101,,,,1143856405,993993009,951829931,1236519669,10039,SRX22238462,SRS19292723,SRA1740017,"Hayes Lab, DSCB, Sickkids Research","Hayes Lab, DSCB, Sickkids Research",1,0.94443,,0.13057,,0.68503,,0.50149,,101,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Canada,2023-10-26,Undetermined,Embryo,Brain,Nervous System 29933,SRR27592958,SRX23261722,SRS20163687,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.,,,,arid1b adult rep15,GSM8020230,,source name:single dissected adult brain male|tissue:single dissected adult brain male|genotype:arid1b homozygous|geo loc name:missing|collection date:missing,arid1b adult rep15,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,single dissected adult brain male,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,tissue:single dissected adult brain male|genotype:arid1b homozygous,GSM8020230,GSM8020230: arid1b adult rep15; Danio rerio; RNA Seq,GSM8020230 r1,GSM8020230,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,arid1b-adult-set2-hom_A8_S20_R1_001.fastq.gz,fastq,4265635010.0,42234010.0,GSM8020230 r1,0:101,A:1152569190;C:1002056793;G:969860357;T:1141141715;N:6955,101,,,,1152569190,1002056793,969860357,1141141715,6955,SRX23261722,SRS20163687,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Adult,Adult,Brain,Nervous System 29934,SRR27592959,SRX23261721,SRS20163686,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.,,,,arid1b adult rep14,GSM8020229,,source name:single dissected adult brain male|tissue:single dissected adult brain male|genotype:arid1b homozygous|geo loc name:missing|collection date:missing,arid1b adult rep14,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,single dissected adult brain male,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,tissue:single dissected adult brain male|genotype:arid1b homozygous,GSM8020229,GSM8020229: arid1b adult rep14; Danio rerio; RNA Seq,GSM8020229 r1,GSM8020229,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,arid1b-adult-set2-hom_A6_S18_R1_001.fastq.gz,fastq,1422969608.0,14088808.0,GSM8020229 r1,0:101,A:389767872;C:327820009;G:327097969;T:378282090;N:1668,101,,,,389767872,327820009,327097969,378282090,1668,SRX23261721,SRS20163686,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Adult,Adult,Brain,Nervous System 29935,SRR27592960,SRX23261720,SRS20163685,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.,,,,arid1b adult rep13,GSM8020228,,source name:single dissected adult brain male|tissue:single dissected adult brain male|genotype:arid1b homozygous|geo loc name:missing|collection date:missing,arid1b adult rep13,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,single dissected adult brain male,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,tissue:single dissected adult brain male|genotype:arid1b homozygous,GSM8020228,GSM8020228: arid1b adult rep13; Danio rerio; RNA Seq,GSM8020228 r1,GSM8020228,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,arid1b-adult-set2-hom_A4_S16_R1_001.fastq.gz,fastq,4331217239.0,42883339.0,GSM8020228 r1,0:101,A:1169654932;C:1016829715;G:986390612;T:1158335000;N:6980,101,,,,1169654932,1016829715,986390612,1158335000,6980,SRX23261720,SRS20163685,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Adult,Adult,Brain,Nervous System 29936,SRR27592961,SRX23261719,SRS20163684,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.,,,,arid1b adult rep12,GSM8020227,,source name:single dissected adult brain male|tissue:single dissected adult brain male|genotype:arid1b homozygous|geo loc name:missing|collection date:missing,arid1b adult rep12,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,single dissected adult brain male,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,tissue:single dissected adult brain male|genotype:arid1b homozygous,GSM8020227,GSM8020227: arid1b adult rep12; Danio rerio; RNA Seq,GSM8020227 r1,GSM8020227,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,arid1b-adult-set2-hom_A2_S14_R1_001.fastq.gz,fastq,820969107.0,8128407.0,GSM8020227 r1,0:101,A:229523100;C:185511734;G:179068656;T:226864374;N:1243,101,,,,229523100,185511734,179068656,226864374,1243,SRX23261719,SRS20163684,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Adult,Adult,Brain,Nervous System 29937,SRR27592962,SRX23261718,SRS20163683,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.,,,,arid1b adult rep11,GSM8020226,,source name:single dissected adult brain male|tissue:single dissected adult brain male|genotype:arid1b heterozygous|geo loc name:missing|collection date:missing,arid1b adult rep11,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,single dissected adult brain male,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,tissue:single dissected adult brain male|genotype:arid1b heterozygous,GSM8020226,GSM8020226: arid1b adult rep11; Danio rerio; RNA Seq,GSM8020226 r1,GSM8020226,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,arid1b-adult-set2-het_A7_S19_R1_001.fastq.gz,fastq,3609957150.0,35742150.0,GSM8020226 r1,0:101,A:997333826;C:818355353;G:803362992;T:990899286;N:5693,101,,,,997333826,818355353,803362992,990899286,5693,SRX23261718,SRS20163683,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Adult,Adult,Brain,Nervous System 29938,SRR27592963,SRX23261717,SRS20163682,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.,,,,arid1b adult rep10,GSM8020225,,source name:single dissected adult brain male|tissue:single dissected adult brain male|genotype:arid1b heterozygous|geo loc name:missing|collection date:missing,arid1b adult rep10,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,single dissected adult brain male,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,tissue:single dissected adult brain male|genotype:arid1b heterozygous,GSM8020225,GSM8020225: arid1b adult rep10; Danio rerio; RNA Seq,GSM8020225 r1,GSM8020225,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,arid1b-adult-set2-het_A5_S17_R1_001.fastq.gz,fastq,3177521913.0,31460613.0,GSM8020225 r1,0:101,A:869322737;C:728803554;G:719191487;T:860199264;N:4871,101,,,,869322737,728803554,719191487,860199264,4871,SRX23261717,SRS20163682,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Adult,Adult,Brain,Nervous System 29939,SRR27592964,SRX23261716,SRS20163681,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.,,,,arid1b adult rep9,GSM8020224,,source name:single dissected adult brain male|tissue:single dissected adult brain male|genotype:arid1b heterozygous|geo loc name:missing|collection date:missing,arid1b adult rep9,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,single dissected adult brain male,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,tissue:single dissected adult brain male|genotype:arid1b heterozygous,GSM8020224,GSM8020224: arid1b adult rep9; Danio rerio; RNA Seq,GSM8020224 r1,GSM8020224,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,arid1b-adult-set2-het_A3_S15_R1_001.fastq.gz,fastq,3681640688.0,36451888.0,GSM8020224 r1,0:101,A:972550652;C:881056608;G:858084187;T:969943492;N:5749,101,,,,972550652,881056608,858084187,969943492,5749,SRX23261716,SRS20163681,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Adult,Adult,Brain,Nervous System 29940,SRR27592965,SRX23261715,SRS20163679,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.,,,,arid1b adult rep8,GSM8020223,,source name:single dissected adult brain male|tissue:single dissected adult brain male|genotype:arid1b heterozygous|geo loc name:missing|collection date:missing,arid1b adult rep8,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,single dissected adult brain male,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,tissue:single dissected adult brain male|genotype:arid1b heterozygous,GSM8020223,GSM8020223: arid1b adult rep8; Danio rerio; RNA Seq,GSM8020223 r1,GSM8020223,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,arid1b-adult-set2-het_A1_S13_R1_001.fastq.gz,fastq,2692714540.0,26660540.0,GSM8020223 r1,0:101,A:739519019;C:619307370;G:594887957;T:738995900;N:4294,101,,,,739519019,619307370,594887957,738995900,4294,SRX23261715,SRS20163679,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Adult,Adult,Brain,Nervous System 29941,SRR27592966,SRX23261714,SRS20163680,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.,,,,arid1b adult rep7,GSM8020222,,source name:single dissected adult brain female|tissue:single dissected adult brain female|genotype:arid1b homozygous|geo loc name:missing|collection date:missing,arid1b adult rep7,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,single dissected adult brain female,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,tissue:single dissected adult brain female|genotype:arid1b homozygous,GSM8020222,GSM8020222: arid1b adult rep7; Danio rerio; RNA Seq,GSM8020222 r1,GSM8020222,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,arid1b-adult-set1-hom_8_S38_R1_001.fastq.gz,fastq,3385303153.0,33517853.0,GSM8020222 r1,0:101,A:922612734;C:831122592;G:725118400;T:906435529;N:13898,101,,,,922612734,831122592,725118400,906435529,13898,SRX23261714,SRS20163680,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Adult,Adult,Brain,Nervous System 29942,SRR27592967,SRX23261713,SRS20163678,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.,,,,arid1b adult rep6,GSM8020221,,source name:single dissected adult brain female|tissue:single dissected adult brain female|genotype:arid1b homozygous|geo loc name:missing|collection date:missing,arid1b adult rep6,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,single dissected adult brain female,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,tissue:single dissected adult brain female|genotype:arid1b homozygous,GSM8020221,GSM8020221: arid1b adult rep6; Danio rerio; RNA Seq,GSM8020221 r1,GSM8020221,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,arid1b-adult-set1-hom_6_S36_R1_001.fastq.gz,fastq,4453651055.0,44095555.0,GSM8020221 r1,0:101,A:1190308155;C:1078598974;G:1012348343;T:1172377706;N:17877,101,,,,1190308155,1078598974,1012348343,1172377706,17877,SRX23261713,SRS20163678,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Adult,Adult,Brain,Nervous System 29943,SRR27592968,SRX23261712,SRS20163677,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.,,,,arid1b adult rep5,GSM8020220,,source name:single dissected adult brain female|tissue:single dissected adult brain female|genotype:arid1b homozygous|geo loc name:missing|collection date:missing,arid1b adult rep5,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,single dissected adult brain female,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,tissue:single dissected adult brain female|genotype:arid1b homozygous,GSM8020220,GSM8020220: arid1b adult rep5; Danio rerio; RNA Seq,GSM8020220 r1,GSM8020220,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,arid1b-adult-set1-hom_5_S35_R1_001.fastq.gz,fastq,3607941998.0,35722198.0,GSM8020220 r1,0:101,A:986679637;C:834475298;G:801712371;T:985059988;N:14704,101,,,,986679637,834475298,801712371,985059988,14704,SRX23261712,SRS20163677,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Adult,Adult,Brain,Nervous System 29944,SRR27592969,SRX23261711,SRS20163675,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.,,,,arid1b adult rep4,GSM8020219,,source name:single dissected adult brain female|tissue:single dissected adult brain female|genotype:arid1b heterozygous|geo loc name:missing|collection date:missing,arid1b adult rep4,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,single dissected adult brain female,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,tissue:single dissected adult brain female|genotype:arid1b heterozygous,GSM8020219,GSM8020219: arid1b adult rep4; Danio rerio; RNA Seq,GSM8020219 r1,GSM8020219,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,arid1b-adult-set1-het_4_S34_R1_001.fastq.gz,fastq,3406563249.0,33728349.0,GSM8020219 r1,0:101,A:929693102;C:825436822;G:742465339;T:908956167;N:11819,101,,,,929693102,825436822,742465339,908956167,11819,SRX23261711,SRS20163675,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Adult,Adult,Brain,Nervous System 29945,SRR27592970,SRX23261710,SRS20163676,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.,,,,arid1b adult rep3,GSM8020218,,source name:single dissected adult brain female|tissue:single dissected adult brain female|genotype:arid1b heterozygous|geo loc name:missing|collection date:missing,arid1b adult rep3,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,single dissected adult brain female,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,tissue:single dissected adult brain female|genotype:arid1b heterozygous,GSM8020218,GSM8020218: arid1b adult rep3; Danio rerio; RNA Seq,GSM8020218 r1,GSM8020218,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,arid1b-adult-set1-het_3_S33_R1_001.fastq.gz,fastq,3437288459.0,34032559.0,GSM8020218 r1,0:101,A:936275875;C:807195445;G:746272516;T:947530775;N:13848,101,,,,936275875,807195445,746272516,947530775,13848,SRX23261710,SRS20163676,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Adult,Adult,Brain,Nervous System 29946,SRR27592971,SRX23261709,SRS20163674,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.,,,,arid1b adult rep2,GSM8020217,,source name:single dissected adult brain female|tissue:single dissected adult brain female|genotype:arid1b heterozygous|geo loc name:missing|collection date:missing,arid1b adult rep2,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,single dissected adult brain female,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,tissue:single dissected adult brain female|genotype:arid1b heterozygous,GSM8020217,GSM8020217: arid1b adult rep2; Danio rerio; RNA Seq,GSM8020217 r1,GSM8020217,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,arid1b-adult-set1-het_2_S32_R1_001.fastq.gz,fastq,3033976067.0,30039367.0,GSM8020217 r1,0:101,A:813028951;C:730788577;G:668973332;T:821173824;N:11383,101,,,,813028951,730788577,668973332,821173824,11383,SRX23261709,SRS20163674,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Adult,Adult,Brain,Nervous System 29971,SRR27592996,SRX23261684,SRS20163649,SRP484215,PRJNA1065838,Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations,GSE253405,Transcriptome Analysis,Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.,,,,arid1b adult rep1,GSM8020216,,source name:single dissected adult brain female|tissue:single dissected adult brain female|genotype:arid1b heterozygous|geo loc name:missing|collection date:missing,arid1b adult rep1,Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.,single dissected adult brain female,,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,tissue:single dissected adult brain female|genotype:arid1b heterozygous,GSM8020216,GSM8020216: arid1b adult rep1; Danio rerio; RNA Seq,GSM8020216 r1,GSM8020216,1,RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484215,,loader:fastq load.py,arid1b-adult-set1-het_1_S31_R1_001.fastq.gz,fastq,2831462785.0,28034285.0,GSM8020216 r1,0:101,A:770779666;C:662406160;G:622932995;T:775332651;N:11313,101,,,,770779666,662406160,622932995,775332651,11313,SRX23261684,SRS20163649,SRA1787174,UMass Chan Medical School,UMass Chan Medical School,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2024-01-16,Adult,Adult,Brain,Nervous System 34554,SRR32104359,SRX27449951,SRS23876473,SRP559533,PRJNA1214751,Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq],GSE287815,Transcriptome Analysis,During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.,,,,17hpf Negative CNC 3,GSM8751784,,source name:non neural crest from midbrain hindbrain boundary to somite 6|tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry |geo loc name:missing|collection date:missing,17hpf Negative CNC 3,Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples,non neural crest from midbrain hindbrain boundary to somite 6,,mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.,,tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry ,GSM8751784,GSM8751784: 17hpf Negative CNC 3; Danio rerio; RNA Seq,GSM8751784 r1,GSM8751784,1,mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP559533,,,Sox10_neg_17hpf_CNC_3_22029_combined_filtered.fastq.gz,fastq,6549316700.0,65493167.0,GSM8751784 r1,0:100,A:1904137226;C:1372226751;G:1395882591;T:1876995541;N:74591,100,,,,1904137226,1372226751,1395882591,1876995541,74591,SRX27449951,SRS23876473,SRA2058978,"Martik Lab, Molecular and Cell Biology, University of California Berkeley","Martik Lab, Molecular and Cell Biology, University of California Berkeley",,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2025-01-23,Segmentation,Embryo,Brain,Nervous System 34555,SRR32104360,SRX27449950,SRS23876471,SRP559533,PRJNA1214751,Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq],GSE287815,Transcriptome Analysis,During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.,,,,17hpf Negative CNC 2,GSM8751783,,source name:non neural crest from midbrain hindbrain boundary to somite 6|tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry |geo loc name:missing|collection date:missing,17hpf Negative CNC 2,Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples,non neural crest from midbrain hindbrain boundary to somite 6,,mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.,,tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry ,GSM8751783,GSM8751783: 17hpf Negative CNC 2; Danio rerio; RNA Seq,GSM8751783 r1,GSM8751783,1,mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP559533,,,Sox10_neg_17hpf_CNC_2_21339_combined_filtered.fastq.gz,fastq,2595442300.0,51908846.0,GSM8751783 r1,0:50,A:735396784;C:561568693;G:572114011;T:726356371;N:6441,50,,,,735396784,561568693,572114011,726356371,6441,SRX27449950,SRS23876471,SRA2058978,"Martik Lab, Molecular and Cell Biology, University of California Berkeley","Martik Lab, Molecular and Cell Biology, University of California Berkeley",,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2025-01-23,Segmentation,Embryo,Brain,Nervous System 34556,SRR32104361,SRX27449949,SRS23876470,SRP559533,PRJNA1214751,Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq],GSE287815,Transcriptome Analysis,During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.,,,,17hpf Negative CNC 1,GSM8751782,,source name:non neural crest from midbrain hindbrain boundary to somite 6|tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry |geo loc name:missing|collection date:missing,17hpf Negative CNC 1,Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples,non neural crest from midbrain hindbrain boundary to somite 6,,mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.,,tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry ,GSM8751782,GSM8751782: 17hpf Negative CNC 1; Danio rerio; RNA Seq,GSM8751782 r1,GSM8751782,1,mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP559533,,,Sox10_neg_17hpf_CNC_1_21310_combined_filtered.fastq.gz,fastq,2554400850.0,51088017.0,GSM8751782 r1,0:50,A:739730182;C:537827580;G:551508245;T:725296198;N:38645,50,,,,739730182,537827580,551508245,725296198,38645,SRX27449949,SRS23876470,SRA2058978,"Martik Lab, Molecular and Cell Biology, University of California Berkeley","Martik Lab, Molecular and Cell Biology, University of California Berkeley",,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2025-01-23,Segmentation,Embryo,Brain,Nervous System 34964,SRR32588721,SRX27895230,SRS24266233,SRP568323,PRJNA1232602,Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains,PRJNA1232602,Other,In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.,,,,Iso Seq RNA from Danio rerio,C2 F2 F B,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from brain,C2 F2 F B,C2 F2 F B,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m64467e_240523_204656.skera.flnc.fastq.gz,fastq,11267908778.0,6337509.0,m64467e 240523 204656.skera.flnc.fastq.gz,0:1777.97,A:3374083285;C:2369790412;G:2399920883;T:3124114198;N:0,1777,,,,3374083285,2369790412,2399920883,3124114198,0,SRX27895230,SRS24266233,SRA2089085,National Human Genome Research Institute|Translational and Functional Genomics Branch,National Human Genome Research Institute National Human Genome Research Institute,,,,,,,,,,,,T,,long read,pacbio,pacbio_modern,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2025-03-06,Adult,Adult,Brain,Nervous System 34973,SRR32588730,SRX27895221,SRS24266225,SRP568323,PRJNA1232602,Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains,PRJNA1232602,Other,In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.,,,,Iso Seq RNA from Danio rerio,C2 F2 M B,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:male|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from brain,C2 F2 M B,C2 F2 M B,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m84270_240904_192359_s4.skera.flnc.fastq.gz,fastq,64391727308.0,29612753.0,m84270 240904 192359 s4.skera.flnc.fastq.gz,0:2174.46,A:18972670876;C:13388478305;G:13738034427;T:18292543700;N:0,2174,,,,18972670876,13388478305,13738034427,18292543700,0,SRX27895221,SRS24266225,SRA2089085,National Human Genome Research Institute|Translational and Functional Genomics Branch,National Human Genome Research Institute National Human Genome Research Institute,,,,,,,,,,,,T,,long read,pacbio,pacbio_modern,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2025-03-06,Adult,Adult,Brain,Nervous System 36363,SRR489486,SRX143563,SRS310284,SRP012376,PRJNA160143,Extensive alternative polyadenylation during zebrafish development,GSE37453,Transcriptome Analysis,The post transcriptional fate of messenger RNAs mRNAs is largely dictated by their three prime' untranslated regions three prime'UTRs which are defined by cleavage and polyadenylation CPA of pre mRNAs. We used polyA position profiling by sequencing 3P Seq to map polyA sites at eight developmental stages and tissues in the zebrafish. Analysis of over 60 million 3P Seq reads substantially increased and improved existing three prime'UTR annotations resulting in confidently identified three prime'UTRs for more than 78.79% of the annotated protein coding genes in zebrafish. Most zebrafish genes undergo alternative CPA with more than a thousand genes using different dominant three prime'UTRs at different stages. three prime'UTRs tend to be shortest in the ovaries and longest in the brain. Isoforms with some of the shortest three prime'UTRs are highly expressed in the ovary yet absent in the maternally contributed RNAs of the embryo perhaps because their three prime'UTRs are too short to accommodate a uridine rich motif required for stability of the maternal mRNA. At two hpf thousands of unique polyA sites appear at locations lacking a typical polyadenylation signal which suggests a wave of widespread cytoplasmic polyadenylation of mRNA degradation intermediates. Our insights into the identities formation and evolution of zebrafish three prime'UTRs provide a resource for studying gene regulation during vertebrate development. Overall design: 3P Seq was used to map the three prime' ends of protein coding genes in the zebrafish genome,,pubmed:22722342,,3P Seq Brain,GSM919969,,source name:mixed gender adults|genotype/variation:wild type|tissue:brain|development stage:adult,3P Seq Brain,For 3P Seq: Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. The BED file is as in Jan et al. GSE24924 For 3P PE Seq: In each read pair read #1 captured the three prime end of the polyA tail in the antisense orientation and read #2 captured a portion of the three prime region of the transcript and occasionally the beginning of the polyA tail in the sense orientation. Read #2 began with an adapter of 26 bases. Reads with more than 10 mismatches to the adapter were discarded and the first 26 bases were removed before further processing. A read pair was considered informative only if read #1 began with Ts and read #2 contained 2–39 terminal As. post leading Ts and terminal As were removed from reads #1 and #2 respectively they were mapped to the genome using Bowtie allowing for up to two mismatches and requiring a unique mapping position in the zebrafish genome. The length of the tail encoded in read #2 was defined as the maximum number of trailing As allowing for up to one mismatch. Only cases in which this number was larger than the number of As encoded in the genome at the predicted cleavage position by at least 2 bases were carried forward. Cleavage and polyadenylation position was defined as the last non A base in read #2. The length of the polyA tail at that position was estimated using the corresponding read #1 and defined as the maximal i for which >90% of the bases in the first i bases of read #1 were Ts. This criterion was used to allow for some sequencing errors expected when sequencing long homopolymers. Genome build: danRer7 Supplementary files format and content: The .bed files contain the positions where 3P Seq reads were mapped and the name of each track is the number of reads mapping to that position. Supplementary files format and content: The bigWig .bw files contain a summary of the number of reads whose three prime ends mapped to each position in the genome. Supplementary files format and content: For the paired end sequencing for mapping polyA tail lengths the text files contain the following columns : chromosome position strand number of polyA length reads followed by the individual measurements lower bounds on polyA tail length,mixed gender adults,Anesthetized decorioneted embryos were washed three times in PBS 137 mM NaCl 2.7 mM KCl 1.5 mM KH2PO4 8 mM Na2HP04 pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed and pellets were rinsed twice with PBS flash frozen in liquid nitrogen and stored at 80C.,3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html,Zebrafish embryos or adults grown under standard condition,genotype/variation:wild type|tissue:brain|developmental stage:adult,GSM919969,GSM919969: 3P Seq Brain; Danio rerio; RNA Seq,GSM919969 1,GSM919969: 3P Seq Brain,1,,GEO Accession:GSM919969,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer II,360Application ReadForward1,SRP012376,,,3P_Seq_Brain.fastq,fastq,592119324.0,16447759.0,GSM919969 r1,0:36,A:231026484;C:109822201;G:93671127;T:157421018;N:178494,36,,,,231026484,109822201,93671127,157421018,178494,SRX143563,SRS310284,SRA051955,GEO,Whitehead Institute for Biomedical Research,1,0.57742,,0.10125,,0.78267,,0.52634,,36,,B,,usable mapping rate,illumina,early_illumina,3prime,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2012-04-20,Adult,Adult,Brain,Nervous System 38228,SRR1565820,SRX692872,SRS694598,SRP046222,PRJNA260259,Neurotranscriptome profiles of four zebrafish strains,GSE61108,Transcriptome Analysis,Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subsequent differential gene expression and network analyses. qRT–PCR validation was performed using SYBR Green assays,,pubmed:25326170;pubmed:26032017;pubmed:26309813,,HSB male rep2,GSM1496860,,tissue:whole brain|strain:High Stationary Behavior|Sex:male|age:17 weeks,HSB male rep2,"Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using ""union"" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample",whole brain,,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,,strain:High Stationary Behavior|Sex:male|age:17 weeks,GSM1496860,GSM1496860: HSB male rep2; Danio rerio; RNA Seq,GSM1496860,,1,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,GEO Accession:GSM1496860,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP046222,,,hsbm2.combined.fastq,fastq,3059139324.0,44987343.0,GSM1496860 r1,0:68,A:856889933;C:683001073;G:664047004;T:854889841;N:311473,68,,,,856889933,683001073,664047004,854889841,311473,SRX692872,SRS694598,SRA181596,GEO,"Biology, University of Nebraska at Omaha",1,0.91541,,0.1123,,0.71194,,0.51402,,68,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,trueseq,bulk,unknown,unknown,,United States,2014-09-04,Adult,Adult,Brain,Nervous System 38229,SRR1565819,SRX692871,SRS694597,SRP046222,PRJNA260259,Neurotranscriptome profiles of four zebrafish strains,GSE61108,Transcriptome Analysis,Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subsequent differential gene expression and network analyses. qRT–PCR validation was performed using SYBR Green assays,,pubmed:25326170;pubmed:26032017;pubmed:26309813,,HSB male rep1,GSM1496859,,tissue:whole brain|strain:High Stationary Behavior|Sex:male|age:17 weeks,HSB male rep1,"Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using ""union"" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample",whole brain,,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,,strain:High Stationary Behavior|Sex:male|age:17 weeks,GSM1496859,GSM1496859: HSB male rep1; Danio rerio; RNA Seq,GSM1496859,,1,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,GEO Accession:GSM1496859,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP046222,,,hsbm1.combined.fastq,fastq,4119155012.0,60575809.0,GSM1496859 r1,0:68,A:1142713472;C:928735770;G:909202318;T:1138084541;N:418911,68,,,,1142713472,928735770,909202318,1138084541,418911,SRX692871,SRS694597,SRA181596,GEO,"Biology, University of Nebraska at Omaha",1,0.91626,,0.10986,,0.71027,,0.51436,,68,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,trueseq,bulk,unknown,unknown,,United States,2014-09-04,Adult,Adult,Brain,Nervous System 38230,SRR1565818,SRX692870,SRS694596,SRP046222,PRJNA260259,Neurotranscriptome profiles of four zebrafish strains,GSE61108,Transcriptome Analysis,Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subsequent differential gene expression and network analyses. qRT–PCR validation was performed using SYBR Green assays,,pubmed:25326170;pubmed:26032017;pubmed:26309813,,HSB female rep2,GSM1496858,,tissue:whole brain|strain:High Stationary Behavior|Sex:female|age:17 weeks,HSB female rep2,"Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using ""union"" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample",whole brain,,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,,strain:High Stationary Behavior|Sex:female|age:17 weeks,GSM1496858,GSM1496858: HSB female rep2; Danio rerio; RNA Seq,GSM1496858,,1,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,GEO Accession:GSM1496858,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP046222,,,hsbf2.combined.fastq,fastq,2322256780.0,34150835.0,GSM1496858 r1,0:68,A:652886524;C:515567581;G:502432518;T:651135720;N:234437,68,,,,652886524,515567581,502432518,651135720,234437,SRX692870,SRS694596,SRA181596,GEO,"Biology, University of Nebraska at Omaha",1,0.91476,,0.11796,,0.70983,,0.51225,,68,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,trueseq,bulk,unknown,unknown,,United States,2014-09-04,Adult,Adult,Brain,Nervous System 38231,SRR1565817,SRX692869,SRS694595,SRP046222,PRJNA260259,Neurotranscriptome profiles of four zebrafish strains,GSE61108,Transcriptome Analysis,Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subsequent differential gene expression and network analyses. qRT–PCR validation was performed using SYBR Green assays,,pubmed:25326170;pubmed:26032017;pubmed:26309813,,HSB female rep1,GSM1496857,,tissue:whole brain|strain:High Stationary Behavior|Sex:female|age:17 weeks,HSB female rep1,"Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using ""union"" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample",whole brain,,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,,strain:High Stationary Behavior|Sex:female|age:17 weeks,GSM1496857,GSM1496857: HSB female rep1; Danio rerio; RNA Seq,GSM1496857,,1,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,GEO Accession:GSM1496857,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP046222,,,hsbf1.combined.fastq,fastq,3760288004.0,55298353.0,GSM1496857 r1,0:68,A:1032777273;C:857978859;G:843770671;T:1025375295;N:385906,68,,,,1032777273,857978859,843770671,1025375295,385906,SRX692869,SRS694595,SRA181596,GEO,"Biology, University of Nebraska at Omaha",1,0.9211,,0.11065,,0.71139,,0.52798,,68,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,trueseq,bulk,unknown,unknown,,United States,2014-09-04,Adult,Adult,Brain,Nervous System 38232,SRR1565816,SRX692868,SRS694594,SRP046222,PRJNA260259,Neurotranscriptome profiles of four zebrafish strains,GSE61108,Transcriptome Analysis,Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subsequent differential gene expression and network analyses. qRT–PCR validation was performed using SYBR Green assays,,pubmed:25326170;pubmed:26032017;pubmed:26309813,,LSB male rep2,GSM1496856,,tissue:whole brain|strain:Low Stationary Behavior|Sex:male|age:17 weeks,LSB male rep2,"Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using ""union"" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample",whole brain,,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,,strain:Low Stationary Behavior|Sex:male|age:17 weeks,GSM1496856,GSM1496856: LSB male rep2; Danio rerio; RNA Seq,GSM1496856,,1,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,GEO Accession:GSM1496856,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP046222,,,lsbm2.combined.fastq,fastq,3620479800.0,53242350.0,GSM1496856 r1,0:68,A:1012281079;C:808037554;G:792170057;T:1007622036;N:369074,68,,,,1012281079,808037554,792170057,1007622036,369074,SRX692868,SRS694594,SRA181596,GEO,"Biology, University of Nebraska at Omaha",1,0.91727,,0.10852,,0.71161,,0.51898,,68,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,trueseq,bulk,unknown,unknown,,United States,2014-09-04,Adult,Adult,Brain,Nervous System 38233,SRR1565815,SRX692867,SRS694593,SRP046222,PRJNA260259,Neurotranscriptome profiles of four zebrafish strains,GSE61108,Transcriptome Analysis,Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subsequent differential gene expression and network analyses. qRT–PCR validation was performed using SYBR Green assays,,pubmed:25326170;pubmed:26032017;pubmed:26309813,,LSB male rep1,GSM1496855,,tissue:whole brain|strain:Low Stationary Behavior|Sex:male|age:17 weeks,LSB male rep1,"Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using ""union"" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample",whole brain,,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,,strain:Low Stationary Behavior|Sex:male|age:17 weeks,GSM1496855,GSM1496855: LSB male rep1; Danio rerio; RNA Seq,GSM1496855,,1,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,GEO Accession:GSM1496855,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP046222,,,lsbm1.combined.fastq,fastq,3939102572.0,57927979.0,GSM1496855 r1,0:68,A:1092436127;C:887516211;G:870661049;T:1088088575;N:400610,68,,,,1092436127,887516211,870661049,1088088575,400610,SRX692867,SRS694593,SRA181596,GEO,"Biology, University of Nebraska at Omaha",1,0.91978,,0.10214,,0.70869,,0.5206,,68,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,trueseq,bulk,unknown,unknown,,United States,2014-09-04,Adult,Adult,Brain,Nervous System 38234,SRR1565814,SRX692866,SRS694592,SRP046222,PRJNA260259,Neurotranscriptome profiles of four zebrafish strains,GSE61108,Transcriptome Analysis,Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subsequent differential gene expression and network analyses. qRT–PCR validation was performed using SYBR Green assays,,pubmed:25326170;pubmed:26032017;pubmed:26309813,,LSB female rep2,GSM1496854,,tissue:whole brain|strain:Low Stationary Behavior|Sex:female|age:17 weeks,LSB female rep2,"Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using ""union"" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample",whole brain,,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,,strain:Low Stationary Behavior|Sex:female|age:17 weeks,GSM1496854,GSM1496854: LSB female rep2; Danio rerio; RNA Seq,GSM1496854,,1,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,GEO Accession:GSM1496854,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP046222,,,lsbf2.combined.fastq,fastq,3396163712.0,49943584.0,GSM1496854 r1,0:68,A:952427292;C:755558175;G:739625271;T:948206206;N:346768,68,,,,952427292,755558175,739625271,948206206,346768,SRX692866,SRS694592,SRA181596,GEO,"Biology, University of Nebraska at Omaha",1,0.91971,,0.09762,,0.7139,,0.53907,,68,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,trueseq,bulk,unknown,unknown,,United States,2014-09-04,Adult,Adult,Brain,Nervous System 38235,SRR1565813,SRX692865,SRS694591,SRP046222,PRJNA260259,Neurotranscriptome profiles of four zebrafish strains,GSE61108,Transcriptome Analysis,Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subsequent differential gene expression and network analyses. qRT–PCR validation was performed using SYBR Green assays,,pubmed:25326170;pubmed:26032017;pubmed:26309813,,LSB female rep1,GSM1496853,,tissue:whole brain|strain:Low Stationary Behavior|Sex:female|age:17 weeks,LSB female rep1,"Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using ""union"" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample",whole brain,,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,,strain:Low Stationary Behavior|Sex:female|age:17 weeks,GSM1496853,GSM1496853: LSB female rep1; Danio rerio; RNA Seq,GSM1496853,,1,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,GEO Accession:GSM1496853,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP046222,,,lsbf1.combined.fastq,fastq,2990889832.0,43983674.0,GSM1496853 r1,0:68,A:834325179;C:670514335;G:655478374;T:830265381;N:306563,68,,,,834325179,670514335,655478374,830265381,306563,SRX692865,SRS694591,SRA181596,GEO,"Biology, University of Nebraska at Omaha",1,0.91961,,0.10554,,0.71058,,0.54194,,68,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,trueseq,bulk,unknown,unknown,,United States,2014-09-04,Adult,Adult,Brain,Nervous System 38236,SRR1565812,SRX692864,SRS694590,SRP046222,PRJNA260259,Neurotranscriptome profiles of four zebrafish strains,GSE61108,Transcriptome Analysis,Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subsequent differential gene expression and network analyses. qRT–PCR validation was performed using SYBR Green assays,,pubmed:25326170;pubmed:26032017;pubmed:26309813,,SH male rep2,GSM1496852,,tissue:whole brain|strain:Scientific Hatcheries|Sex:male|age:17 weeks,SH male rep2,"Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using ""union"" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample",whole brain,,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,,strain:Scientific Hatcheries|Sex:male|age:17 weeks,GSM1496852,GSM1496852: SH male rep2; Danio rerio; RNA Seq,GSM1496852,,1,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,GEO Accession:GSM1496852,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP046222,,,shm2.combined.fastq,fastq,3027917260.0,44528195.0,GSM1496852 r1,0:68,A:849520890;C:674435387;G:655632316;T:848019818;N:308849,68,,,,849520890,674435387,655632316,848019818,308849,SRX692864,SRS694590,SRA181596,GEO,"Biology, University of Nebraska at Omaha",1,0.91854,,0.11844,,0.70914,,0.52599,,68,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,trueseq,bulk,unknown,unknown,,United States,2014-09-04,Adult,Adult,Brain,Nervous System 38237,SRR1565811,SRX692863,SRS694589,SRP046222,PRJNA260259,Neurotranscriptome profiles of four zebrafish strains,GSE61108,Transcriptome Analysis,Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subsequent differential gene expression and network analyses. qRT–PCR validation was performed using SYBR Green assays,,pubmed:25326170;pubmed:26032017;pubmed:26309813,,SH male rep1,GSM1496851,,tissue:whole brain|strain:Scientific Hatcheries|Sex:male|age:17 weeks,SH male rep1,"Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using ""union"" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample",whole brain,,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,,strain:Scientific Hatcheries|Sex:male|age:17 weeks,GSM1496851,GSM1496851: SH male rep1; Danio rerio; RNA Seq,GSM1496851,,1,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,GEO Accession:GSM1496851,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP046222,,,shm1.combined.fastq,fastq,4020657964.0,59127323.0,GSM1496851 r1,0:68,A:1118924354;C:902394021;G:884260445;T:1114671095;N:408049,68,,,,1118924354,902394021,884260445,1114671095,408049,SRX692863,SRS694589,SRA181596,GEO,"Biology, University of Nebraska at Omaha",1,0.92006,,0.11336,,0.70757,,0.52355,,68,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,trueseq,bulk,unknown,unknown,,United States,2014-09-04,Adult,Adult,Brain,Nervous System 38238,SRR1565810,SRX692862,SRS694588,SRP046222,PRJNA260259,Neurotranscriptome profiles of four zebrafish strains,GSE61108,Transcriptome Analysis,Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subsequent differential gene expression and network analyses. qRT–PCR validation was performed using SYBR Green assays,,pubmed:25326170;pubmed:26032017;pubmed:26309813,,SH female rep2,GSM1496850,,tissue:whole brain|strain:Scientific Hatcheries|Sex:female|age:17 weeks,SH female rep2,"Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using ""union"" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample",whole brain,,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,,strain:Scientific Hatcheries|Sex:female|age:17 weeks,GSM1496850,GSM1496850: SH female rep2; Danio rerio; RNA Seq,GSM1496850,,1,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,GEO Accession:GSM1496850,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP046222,,,shf2.combined.fastq,fastq,4142523076.0,60919457.0,GSM1496850 r1,0:68,A:1153819987;C:929925663;G:908337889;T:1150019261;N:420276,68,,,,1153819987,929925663,908337889,1150019261,420276,SRX692862,SRS694588,SRA181596,GEO,"Biology, University of Nebraska at Omaha",1,0.91937,,0.1168,,0.70936,,0.50937,,68,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,trueseq,bulk,unknown,unknown,,United States,2014-09-04,Adult,Adult,Brain,Nervous System 38239,SRR1565809,SRX692861,SRS694587,SRP046222,PRJNA260259,Neurotranscriptome profiles of four zebrafish strains,GSE61108,Transcriptome Analysis,Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subsequent differential gene expression and network analyses. qRT–PCR validation was performed using SYBR Green assays,,pubmed:25326170;pubmed:26032017;pubmed:26309813,,SH female rep1,GSM1496849,,tissue:whole brain|strain:Scientific Hatcheries|Sex:female|age:17 weeks,SH female rep1,"Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using ""union"" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample",whole brain,,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,,strain:Scientific Hatcheries|Sex:female|age:17 weeks,GSM1496849,GSM1496849: SH female rep1; Danio rerio; RNA Seq,GSM1496849,,1,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,GEO Accession:GSM1496849,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP046222,,,shf1.combined.fastq,fastq,4453572076.0,65493707.0,GSM1496849 r1,0:68,A:1240033407;C:999435900;G:979449791;T:1234195169;N:457809,68,,,,1240033407,999435900,979449791,1234195169,457809,SRX692861,SRS694587,SRA181596,GEO,"Biology, University of Nebraska at Omaha",1,0.92108,,0.11284,,0.70678,,0.52548,,68,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,trueseq,bulk,unknown,unknown,,United States,2014-09-04,Adult,Adult,Brain,Nervous System 38240,SRR1565808,SRX692860,SRS694586,SRP046222,PRJNA260259,Neurotranscriptome profiles of four zebrafish strains,GSE61108,Transcriptome Analysis,Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subsequent differential gene expression and network analyses. qRT–PCR validation was performed using SYBR Green assays,,pubmed:25326170;pubmed:26032017;pubmed:26309813,,AB male rep2,GSM1496848,,tissue:whole brain|strain:AB|Sex:male|age:17 weeks,AB male rep2,"Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using ""union"" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample",whole brain,,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,,strain:AB|Sex:male|age:17 weeks,GSM1496848,GSM1496848: AB male rep2; Danio rerio; RNA Seq,GSM1496848,,1,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,GEO Accession:GSM1496848,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP046222,,,abm2.combined.fastq,fastq,2872717120.0,42245840.0,GSM1496848 r1,0:68,A:804944428;C:640905199;G:622289037;T:804286004;N:292452,68,,,,804944428,640905199,622289037,804286004,292452,SRX692860,SRS694586,SRA181596,GEO,"Biology, University of Nebraska at Omaha",1,0.92023,,0.11215,,0.71133,,0.51311,,68,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,trueseq,bulk,unknown,unknown,,United States,2014-09-04,Adult,Adult,Brain,Nervous System 38241,SRR1565807,SRX692859,SRS694585,SRP046222,PRJNA260259,Neurotranscriptome profiles of four zebrafish strains,GSE61108,Transcriptome Analysis,Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subsequent differential gene expression and network analyses. qRT–PCR validation was performed using SYBR Green assays,,pubmed:25326170;pubmed:26032017;pubmed:26309813,,AB male rep1,GSM1496847,,tissue:whole brain|strain:AB|Sex:male|age:17 weeks,AB male rep1,"Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using ""union"" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample",whole brain,,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,,strain:AB|Sex:male|age:17 weeks,GSM1496847,GSM1496847: AB male rep1; Danio rerio; RNA Seq,GSM1496847,,1,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,GEO Accession:GSM1496847,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP046222,,,abm1.combined.fastq,fastq,3563207208.0,52400106.0,GSM1496847 r1,0:68,A:995828497;C:796660231;G:778836484;T:991520791;N:361205,68,,,,995828497,796660231,778836484,991520791,361205,SRX692859,SRS694585,SRA181596,GEO,"Biology, University of Nebraska at Omaha",1,0.92353,,0.10674,,0.70918,,0.52999,,68,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,trueseq,bulk,unknown,unknown,,United States,2014-09-04,Adult,Adult,Brain,Nervous System 38242,SRR1565806,SRX692858,SRS694584,SRP046222,PRJNA260259,Neurotranscriptome profiles of four zebrafish strains,GSE61108,Transcriptome Analysis,Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subsequent differential gene expression and network analyses. qRT–PCR validation was performed using SYBR Green assays,,pubmed:25326170;pubmed:26032017;pubmed:26309813,,AB female rep2,GSM1496846,,tissue:whole brain|strain:AB|Sex:female|age:17 weeks,AB female rep2,"Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using ""union"" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample",whole brain,,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,,strain:AB|Sex:female|age:17 weeks,GSM1496846,GSM1496846: AB female rep2; Danio rerio; RNA Seq,GSM1496846,,1,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,GEO Accession:GSM1496846,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP046222,,,abf2.combined.fastq,fastq,3300678452.0,48539389.0,GSM1496846 r1,0:68,A:924872216;C:737186484;G:715434941;T:922846788;N:338023,68,,,,924872216,737186484,715434941,922846788,338023,SRX692858,SRS694584,SRA181596,GEO,"Biology, University of Nebraska at Omaha",1,0.92017,,0.11305,,0.7082,,0.50792,,68,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,trueseq,bulk,unknown,unknown,,United States,2014-09-04,Adult,Adult,Brain,Nervous System 38243,SRR1565805,SRX692857,SRS694583,SRP046222,PRJNA260259,Neurotranscriptome profiles of four zebrafish strains,GSE61108,Transcriptome Analysis,Zebrafish is a model system being used in a variety of basic research and biomedical studies. Understanding the neurotranscriptomic architecture will greatly facilitate and enhance interpretation of research projects. Studies have reported that there are strain and sex specific behavioral variation particulary in response to stress and anxiety inducing scenarios. Capitalizing on previously documented behavioral variation by strains and sex of zebrafish this study seeks to understand the neurotranscriptomic mechanisms potentially underlying this variation. Through RNA sequencing 4 biological replicates per strain further subdivided into 2 biological replicates per sex we analyzed the whole brain transcriptomic profiles of four strains of zebrafish and relate transcriptional differences to phenotypic differences e.g. behavioral or morphological of the strains. Using a balanced block design all 16 samples were multiplexed and run across 16 lanes on an Illumina GAIIx. Resulting reads approximately 52 million reads per biological replicate were aligned to the Zv9 genome build. We subsequently performed differential gene expression analysis and weighted gene coexpression network analysis to identify genes and gene networks associated with a phenotype. The goal of the study is to identify neurotranscriptomic mechanisms underlying phenotypic e.g. morphological behavioral variation in zebrafish. Overall design: Through RNA sequencing we quantified whole brain transcriptome levels of protein coding genes for four strains of zebrafish AB Scientific Hatcheries High Stationary Behavior and Low Stationary Behavior. Each line has 4 biological replicates 2 biological replicates for each sex. Each biological replicate is comprised of a pool of 10 same sex and age matched individuals. Using a balanced block design the samples were mulitplexed and run across 16 lanes on an Illumina GAIIx. Reads that passed default quality control filters were aligned using GSNAP and quantified with HTSEQ. We used edgeR and WGCNA for subsequent differential gene expression and network analyses. qRT–PCR validation was performed using SYBR Green assays,,pubmed:25326170;pubmed:26032017;pubmed:26309813,,AB female rep1,GSM1496845,,tissue:whole brain|strain:AB|Sex:female|age:17 weeks,AB female rep1,"Illumina Casava 1.7 software used for basecalling. Reads were aligned using GSNAP Reads were quantified with HTSEQ using ""union"" mode Reads for each gene was normalized by library size. Counts per million reads CPM were calculated with edgeR Genome build: Zv9 Supplementary files format and content: tab delimited text file include CPM values for each Sample",whole brain,,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,,strain:AB|Sex:female|age:17 weeks,GSM1496845,GSM1496845: AB female rep1; Danio rerio; RNA Seq,GSM1496845,,1,Brains were removed placed in RNAlater overnight at 4C. Excess RNAlater was subsequently removed and the brains stoed at 80C until total RNA extraction. Total RNA was extracted using RNeasy Plus Mini kit Qiagen. We pooled 1 ug of total RNA from 10 same sex and same strain individuals into one biological replicate. We followed Illumina TruSeq RNA Sample Prep V2 protocol using 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols for multiplexing. Adapter sequences are as follows: lsbf1 GTGAAAC; lsbf2 GTTTCGG; lsbm1 GTCCGCA; lsbm2 GTGGCCT; hsbf1 CCGTCCC; hsbf2 GGCTACA; hsbm1 ATGTCAG; hsbm2 TAGCTTA; abf1 ATTCCTT; abf2 GATCAGA; abm1 ACTGATA; abm2 ACTTGAA; shf1 GAGTGGA; shf2 TTAGGCA; shm1 CGTACGT; shm2 ATCACGA,GEO Accession:GSM1496845,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP046222,,,abf1.combined.fastq,fastq,4306679496.0,63333522.0,GSM1496845 r1,0:68,A:1203446722;C:961797198;G:943144171;T:1197856637;N:434768,68,,,,1203446722,961797198,943144171,1197856637,434768,SRX692857,SRS694583,SRA181596,GEO,"Biology, University of Nebraska at Omaha",1,0.92127,,0.1098,,0.70757,,0.50805,,68,,B,,usable mapping rate,illumina,early_illumina,full_length,random_priming,trueseq,bulk,unknown,unknown,,United States,2014-09-04,Adult,Adult,Brain,Nervous System 38281,SRR1611974,SRX732528,SRS721348,SRP048902,PRJNA263811,Gene expression profiling of Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999t zebrafish embryos at 3 dpf,GSE62273,Transcriptome Analysis,We use next generation sequencing of embryos with neuronally expressed EWSR1 ERG at 3 dpf to investigate overlap between these embryos' regulated gene set and that of other Ewing sarcoma models Overall design: This deep sequence study was designed to determine the gene expression profile regulated by EWSR1 ERG. Samples were obtained at 3 days post fetilisation from Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999tRNA embryos expressing EWSR1 ERG neuronally or wild type siblings. RNA was isolated from 15 embryos per sample using the RNeasy Micro Kit Qiagen.,,,,8 dpf 3 dpf embryo neuronally expressing EWSR1 ERG,GSM1524335,,tissue:Danio rerio embryo Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999t 3 dpf with neuronally expressed EWSR1 ERG|biological replica:3,8 dpf 3 dpf embryo neuronally expressing EWSR1 ERG,GeneTiles was used for quantification and visualization of the RNAseq data Bowtie2 is used to align the reads in the fastq file to the genome obtained from Ensemble. Bowtie2 generates SAM files that contain the reads together with the location on the genome. Samtools is used to convert and compress the SAM files into a binary BAM file. Samtools is furthermore used to sort the reads in the BAM files based on the aligned read location in the genome resulting in a sorted BAM file. The BAM files is indexed to be able to quickly find the aligned reads based on a location in the genome i.e. to be able to quickly search the BAM file. The index is a saved as a BAI file. Using the available annotation from Ensemble we can search the BAM file for reads within a gene using exon starting positions and lengths. This is done with a python script. The output of this script is a tab separated file tsv containing the read counts per gene. We used DESeq an R script to perform statistical analysis. The DESeq script is used to normalise the reads per gene based on divided by the total number of reads obtained per sample. Then variance and average of the measurement compared to the control can be expressed as a P value by calculating the dispersion per gene using DESeq. The size factors as well as the P values are stored in ‘tsv’ files. Using a script all tsv files are combined into tsv files e.g. per experiment chromosome per filtered results of most significant reads or highest ratio between measurement and control. Genome build: Zv9 toplevel,Danio rerio embryo Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999t 3 dpf,,Embryos for RNA isolation were homogenized using Bullet Blender Homogenizer Next Advance Averill Park NY; subsequently RNA was extracted using the RNeasy Micro Kit Qiagen according to the manufacturer’s instructions and stored at 80°C. The integrity of the RNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts.,genotype/variation:Embryos with neuronally expressed EWSR1 ERG|biological replica:3,GSM1524335,GSM1524335: 8 dpf 3 dpf embryo neuronally expressing EWSR1 ERG; Danio rerio; RNA Seq,GSM1524335,,1,Embryos for RNA isolation were homogenized using Bullet Blender Homogenizer Next Advance Averill Park NY; subsequently RNA was extracted using the RNeasy Micro Kit Qiagen according to the manufacturer’s instructions and stored at 80°C. The integrity of the RNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1524335,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP048902,,,,,878388453.0,17223303.0,GSM1524335 r1,0:51,A:232302914;C:211453624;G:203524178;T:231030317;N:77420,51,,,,232302914,211453624,203524178,231030317,77420,SRX732528,SRS721348,SRA190781,GEO,"Leiden University, Institute of Biology Leiden",1,0.93382,,0.06489,,0.69871,,0.43941,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2014-10-10,Larval,Larval,Brain,Nervous System 38282,SRR1611973,SRX732527,SRS721347,SRP048902,PRJNA263811,Gene expression profiling of Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999t zebrafish embryos at 3 dpf,GSE62273,Transcriptome Analysis,We use next generation sequencing of embryos with neuronally expressed EWSR1 ERG at 3 dpf to investigate overlap between these embryos' regulated gene set and that of other Ewing sarcoma models Overall design: This deep sequence study was designed to determine the gene expression profile regulated by EWSR1 ERG. Samples were obtained at 3 days post fetilisation from Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999tRNA embryos expressing EWSR1 ERG neuronally or wild type siblings. RNA was isolated from 15 embryos per sample using the RNeasy Micro Kit Qiagen.,,,,7 dpf 3 dpf embryo neuronally expressing EWSR1 ERG,GSM1524334,,tissue:Danio rerio embryo Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999t 3 dpf with neuronally expressed EWSR1 ERG|biological replica:2,7 dpf 3 dpf embryo neuronally expressing EWSR1 ERG,GeneTiles was used for quantification and visualization of the RNAseq data Bowtie2 is used to align the reads in the fastq file to the genome obtained from Ensemble. Bowtie2 generates SAM files that contain the reads together with the location on the genome. Samtools is used to convert and compress the SAM files into a binary BAM file. Samtools is furthermore used to sort the reads in the BAM files based on the aligned read location in the genome resulting in a sorted BAM file. The BAM files is indexed to be able to quickly find the aligned reads based on a location in the genome i.e. to be able to quickly search the BAM file. The index is a saved as a BAI file. Using the available annotation from Ensemble we can search the BAM file for reads within a gene using exon starting positions and lengths. This is done with a python script. The output of this script is a tab separated file tsv containing the read counts per gene. We used DESeq an R script to perform statistical analysis. The DESeq script is used to normalise the reads per gene based on divided by the total number of reads obtained per sample. Then variance and average of the measurement compared to the control can be expressed as a P value by calculating the dispersion per gene using DESeq. The size factors as well as the P values are stored in ‘tsv’ files. Using a script all tsv files are combined into tsv files e.g. per experiment chromosome per filtered results of most significant reads or highest ratio between measurement and control. Genome build: Zv9 toplevel,Danio rerio embryo Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999t 3 dpf,,Embryos for RNA isolation were homogenized using Bullet Blender Homogenizer Next Advance Averill Park NY; subsequently RNA was extracted using the RNeasy Micro Kit Qiagen according to the manufacturer’s instructions and stored at 80°C. The integrity of the RNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts.,genotype/variation:Embryos with neuronally expressed EWSR1 ERG|biological replica:2,GSM1524334,GSM1524334: 7 dpf 3 dpf embryo neuronally expressing EWSR1 ERG; Danio rerio; RNA Seq,GSM1524334,,1,Embryos for RNA isolation were homogenized using Bullet Blender Homogenizer Next Advance Averill Park NY; subsequently RNA was extracted using the RNeasy Micro Kit Qiagen according to the manufacturer’s instructions and stored at 80°C. The integrity of the RNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1524334,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP048902,,,,,372336108.0,7300708.0,GSM1524334 r1,0:51,A:98058295;C:90306461;G:86107301;T:97818336;N:45715,51,,,,98058295,90306461,86107301,97818336,45715,SRX732527,SRS721347,SRA190781,GEO,"Leiden University, Institute of Biology Leiden",1,0.93316,,0.06305,,0.69258,,0.45864,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2014-10-10,Larval,Larval,Brain,Nervous System 38283,SRR1611972,SRX732526,SRS721346,SRP048902,PRJNA263811,Gene expression profiling of Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999t zebrafish embryos at 3 dpf,GSE62273,Transcriptome Analysis,We use next generation sequencing of embryos with neuronally expressed EWSR1 ERG at 3 dpf to investigate overlap between these embryos' regulated gene set and that of other Ewing sarcoma models Overall design: This deep sequence study was designed to determine the gene expression profile regulated by EWSR1 ERG. Samples were obtained at 3 days post fetilisation from Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999tRNA embryos expressing EWSR1 ERG neuronally or wild type siblings. RNA was isolated from 15 embryos per sample using the RNeasy Micro Kit Qiagen.,,,,6 dpf 3 dpf embryo neuronally expressing EWSR1 ERG,GSM1524333,,tissue:Danio rerio embryo Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999t 3 dpf with neuronally expressed EWSR1 ERG|biological replica:1,6 dpf 3 dpf embryo neuronally expressing EWSR1 ERG,GeneTiles was used for quantification and visualization of the RNAseq data Bowtie2 is used to align the reads in the fastq file to the genome obtained from Ensemble. Bowtie2 generates SAM files that contain the reads together with the location on the genome. Samtools is used to convert and compress the SAM files into a binary BAM file. Samtools is furthermore used to sort the reads in the BAM files based on the aligned read location in the genome resulting in a sorted BAM file. The BAM files is indexed to be able to quickly find the aligned reads based on a location in the genome i.e. to be able to quickly search the BAM file. The index is a saved as a BAI file. Using the available annotation from Ensemble we can search the BAM file for reads within a gene using exon starting positions and lengths. This is done with a python script. The output of this script is a tab separated file tsv containing the read counts per gene. We used DESeq an R script to perform statistical analysis. The DESeq script is used to normalise the reads per gene based on divided by the total number of reads obtained per sample. Then variance and average of the measurement compared to the control can be expressed as a P value by calculating the dispersion per gene using DESeq. The size factors as well as the P values are stored in ‘tsv’ files. Using a script all tsv files are combined into tsv files e.g. per experiment chromosome per filtered results of most significant reads or highest ratio between measurement and control. Genome build: Zv9 toplevel,Danio rerio embryo Tg14xUAS:GFP EWSR1 ERG x EtE1b:Gal4 VP16s1101t TgUAS:Kaede s1999t 3 dpf,,Embryos for RNA isolation were homogenized using Bullet Blender Homogenizer Next Advance Averill Park NY; subsequently RNA was extracted using the RNeasy Micro Kit Qiagen according to the manufacturer’s instructions and stored at 80°C. The integrity of the RNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. RNA libraries were prepared for sequencing using standard Illumina protocols,Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts.,genotype/variation:Embryos with neuronally expressed EWSR1 ERG|biological replica:1,GSM1524333,GSM1524333: 6 dpf 3 dpf embryo neuronally expressing EWSR1 ERG; Danio rerio; RNA Seq,GSM1524333,,1,Embryos for RNA isolation were homogenized using Bullet Blender Homogenizer Next Advance Averill Park NY; subsequently RNA was extracted using the RNeasy Micro Kit Qiagen according to the manufacturer’s instructions and stored at 80°C. The integrity of the RNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1524333,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP048902,,,,,426266619.0,8358169.0,GSM1524333 r1,0:51,A:112004069;C:103380899;G:98829082;T:112000953;N:51616,51,,,,112004069,103380899,98829082,112000953,51616,SRX732526,SRS721346,SRA190781,GEO,"Leiden University, Institute of Biology Leiden",1,0.93027,,0.05803,,0.69493,,0.45892,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2014-10-10,Larval,Larval,Brain,Nervous System 38433,SRR1821806,SRX893407,SRS859560,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,,brain208 36m 3.75nM roten1 8w rep6,GSM1620953,,source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:3.75nM roten1|duration:8 weeks,brain208 36m 3.75nM roten1 8w rep6,FASTQ files were extracted using Illumina Casava software v1.8.2.,total RNA extracted from brain,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:brain|age:36 month|treatment:3.75nM roten1|duration:8 weeks,GSM1620953,GSM1620953: brain208 36m 3.75nM roten1 8w rep6; Danio rerio; RNA Seq,GSM1620953,,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:GSM1620953,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP055573,,,Brain208.fastq.gz,fastq,2306705950.0,46134119.0,GSM1620953 r1,0:50,A:636241272;C:516611728;G:510644879;T:638016950;N:5191121,50,,,,636241272,516611728,510644879,638016950,5191121,SRX893407,SRS859560,SRA244883,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.91528,,0.15975,,0.68972,,0.50406,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2015-02-27,Adult,Adult,Brain,Nervous System 38434,SRR1821805,SRX893406,SRS859561,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,,brain207 36m 3.75nM roten1 8w rep5,GSM1620952,,source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:3.75nM roten1|duration:8 weeks,brain207 36m 3.75nM roten1 8w rep5,FASTQ files were extracted using Illumina Casava software v1.8.2.,total RNA extracted from brain,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:brain|age:36 month|treatment:3.75nM roten1|duration:8 weeks,GSM1620952,GSM1620952: brain207 36m 3.75nM roten1 8w rep5; Danio rerio; RNA Seq,GSM1620952,,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:GSM1620952,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP055573,,,Brain207.fastq.gz,fastq,4144137850.0,82882757.0,GSM1620952 r1,0:50,A:1136843305;C:933236558;G:925158648;T:1139244251;N:9655088,50,,,,1136843305,933236558,925158648,1139244251,9655088,SRX893406,SRS859561,SRA244883,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.90727,,0.15677,,0.69337,,0.51526,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2015-02-27,Adult,Adult,Brain,Nervous System 38435,SRR1821804,SRX893405,SRS859562,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,,brain206 36m 3.75nM roten1 8w rep4,GSM1620951,,source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:3.75nM roten1|duration:8 weeks,brain206 36m 3.75nM roten1 8w rep4,FASTQ files were extracted using Illumina Casava software v1.8.2.,total RNA extracted from brain,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:brain|age:36 month|treatment:3.75nM roten1|duration:8 weeks,GSM1620951,GSM1620951: brain206 36m 3.75nM roten1 8w rep4; Danio rerio; RNA Seq,GSM1620951,,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:GSM1620951,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP055573,,,Brain206.fastq.gz,fastq,2682905100.0,53658102.0,GSM1620951 r1,0:50,A:743936961;C:601044963;G:590021623;T:747739178;N:162375,50,,,,743936961,601044963,590021623,747739178,162375,SRX893405,SRS859562,SRA244883,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.91613,,0.16946,,0.68832,,0.50195,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2015-02-27,Adult,Adult,Brain,Nervous System 38436,SRR1821803,SRX893404,SRS859563,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,,brain205 36m 3.75nM roten1 8w rep3,GSM1620950,,source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:3.75nM roten1|duration:8 weeks,brain205 36m 3.75nM roten1 8w rep3,FASTQ files were extracted using Illumina Casava software v1.8.2.,total RNA extracted from brain,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:brain|age:36 month|treatment:3.75nM roten1|duration:8 weeks,GSM1620950,GSM1620950: brain205 36m 3.75nM roten1 8w rep3; Danio rerio; RNA Seq,GSM1620950,,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:GSM1620950,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP055573,,,Brain205.fastq.gz,fastq,2157560400.0,43151208.0,GSM1620950 r1,0:50,A:599901370;C:482413446;G:470301148;T:604895547;N:48889,50,,,,599901370,482413446,470301148,604895547,48889,SRX893404,SRS859563,SRA244883,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.91687,,0.17871,,0.686,,0.50634,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2015-02-27,Adult,Adult,Brain,Nervous System 38437,SRR1821802,SRX893403,SRS859564,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,,brain204 36m 3.75nM roten1 8w rep2,GSM1620949,,source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:3.75nM roten1|duration:8 weeks,brain204 36m 3.75nM roten1 8w rep2,FASTQ files were extracted using Illumina Casava software v1.8.2.,total RNA extracted from brain,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:brain|age:36 month|treatment:3.75nM roten1|duration:8 weeks,GSM1620949,GSM1620949: brain204 36m 3.75nM roten1 8w rep2; Danio rerio; RNA Seq,GSM1620949,,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:GSM1620949,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP055573,,,Brain204.fastq.gz,fastq,2694973850.0,53899477.0,GSM1620949 r1,0:50,A:743344230;C:608541970;G:595308513;T:747727739;N:51398,50,,,,743344230,608541970,595308513,747727739,51398,SRX893403,SRS859564,SRA244883,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.91086,,0.17132,,0.69471,,0.50107,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2015-02-27,Adult,Adult,Brain,Nervous System 38438,SRR1821801,SRX893402,SRS859565,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,,brain203 36m 3.75nM roten1 8w rep1,GSM1620948,,source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:3.75nM roten1|duration:8 weeks,brain203 36m 3.75nM roten1 8w rep1,FASTQ files were extracted using Illumina Casava software v1.8.2.,total RNA extracted from brain,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:brain|age:36 month|treatment:3.75nM roten1|duration:8 weeks,GSM1620948,GSM1620948: brain203 36m 3.75nM roten1 8w rep1; Danio rerio; RNA Seq,GSM1620948,,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:GSM1620948,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP055573,,,Brain203.fastq.gz,fastq,2853634750.0,57072695.0,GSM1620948 r1,0:50,A:792033384;C:637485994;G:629768204;T:794292474;N:54694,50,,,,792033384,637485994,629768204,794292474,54694,SRX893402,SRS859565,SRA244883,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.91711,,0.16964,,0.68809,,0.50902,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2015-02-27,Adult,Adult,Brain,Nervous System 38439,SRR1821800,SRX893401,SRS859566,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,,brain172 36m 3.75nM roten1 3w rep5,GSM1620947,,source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:3.75nM roten1|duration:3 weeks,brain172 36m 3.75nM roten1 3w rep5,FASTQ files were extracted using Illumina Casava software v1.8.2.,total RNA extracted from brain,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:brain|age:36 month|treatment:3.75nM roten1|duration:3 weeks,GSM1620947,GSM1620947: brain172 36m 3.75nM roten1 3w rep5; Danio rerio; RNA Seq,GSM1620947,,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:GSM1620947,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP055573,,,Brain172.fastq.gz,fastq,1847093550.0,36941871.0,GSM1620947 r1,0:50,A:512828564;C:413023682;G:405063489;T:516143305;N:34510,50,,,,512828564,413023682,405063489,516143305,34510,SRX893401,SRS859566,SRA244883,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.91332,,0.16726,,0.69219,,0.50709,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2015-02-27,Adult,Adult,Brain,Nervous System 38440,SRR1821799,SRX893400,SRS859567,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,,brain171 36m 3.75nM roten1 3w rep4,GSM1620946,,source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:3.75nM roten1|duration:3 weeks,brain171 36m 3.75nM roten1 3w rep4,FASTQ files were extracted using Illumina Casava software v1.8.2.,total RNA extracted from brain,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:brain|age:36 month|treatment:3.75nM roten1|duration:3 weeks,GSM1620946,GSM1620946: brain171 36m 3.75nM roten1 3w rep4; Danio rerio; RNA Seq,GSM1620946,,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:GSM1620946,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP055573,,,Brain171.fastq.gz,fastq,2115110500.0,42302210.0,GSM1620946 r1,0:50,A:605803255;C:456285353;G:449264746;T:603715506;N:41640,50,,,,605803255,456285353,449264746,603715506,41640,SRX893400,SRS859567,SRA244883,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.92083,,0.15603,,0.71752,,0.53696,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2015-02-27,Adult,Adult,Brain,Nervous System 38441,SRR1821798,SRX893399,SRS859568,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,,brain170 36m 3.75nM roten1 3w rep3,GSM1620945,,source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:3.75nM roten1|duration:3 weeks,brain170 36m 3.75nM roten1 3w rep3,FASTQ files were extracted using Illumina Casava software v1.8.2.,total RNA extracted from brain,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:brain|age:36 month|treatment:3.75nM roten1|duration:3 weeks,GSM1620945,GSM1620945: brain170 36m 3.75nM roten1 3w rep3; Danio rerio; RNA Seq,GSM1620945,,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:GSM1620945,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP055573,,,Brain170.fastq.gz,fastq,1954824850.0,39096497.0,GSM1620945 r1,0:50,A:550573629;C:429779639;G:422566533;T:551846246;N:58803,50,,,,550573629,429779639,422566533,551846246,58803,SRX893399,SRS859568,SRA244883,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.91485,,0.15534,,0.69863,,0.51851,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2015-02-27,Adult,Adult,Brain,Nervous System 38442,SRR1821797,SRX893398,SRS859569,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,,brain169 36m 3.75nM roten1 3w rep2,GSM1620944,,source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:3.75nM roten1|duration:3 weeks,brain169 36m 3.75nM roten1 3w rep2,FASTQ files were extracted using Illumina Casava software v1.8.2.,total RNA extracted from brain,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:brain|age:36 month|treatment:3.75nM roten1|duration:3 weeks,GSM1620944,GSM1620944: brain169 36m 3.75nM roten1 3w rep2; Danio rerio; RNA Seq,GSM1620944,,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:GSM1620944,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP055573,,,Brain169.fastq.gz,fastq,1849506700.0,36990134.0,GSM1620944 r1,0:50,A:515047742;C:412800018;G:402098235;T:518926309;N:634396,50,,,,515047742,412800018,402098235,518926309,634396,SRX893398,SRS859569,SRA244883,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.91857,,0.1714,,0.69069,,0.53039,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2015-02-27,Adult,Adult,Brain,Nervous System 38443,SRR1821796,SRX893397,SRS859570,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,,brain168 36m 3.75nM roten1 3w rep1,GSM1620943,,source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:3.75nM roten1|duration:3 weeks,brain168 36m 3.75nM roten1 3w rep1,FASTQ files were extracted using Illumina Casava software v1.8.2.,total RNA extracted from brain,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:brain|age:36 month|treatment:3.75nM roten1|duration:3 weeks,GSM1620943,GSM1620943: brain168 36m 3.75nM roten1 3w rep1; Danio rerio; RNA Seq,GSM1620943,,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:GSM1620943,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP055573,,,Brain168.fastq.gz,fastq,2080177550.0,41603551.0,GSM1620943 r1,0:50,A:581188271;C:463464308;G:451483040;T:583963411;N:78520,50,,,,581188271,463464308,451483040,583963411,78520,SRX893397,SRS859570,SRA244883,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.91585,,0.1671,,0.69487,,0.51506,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2015-02-27,Adult,Adult,Brain,Nervous System 38444,SRR1821795,SRX893396,SRS859571,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,,brain188 36m control 8w rep4,GSM1620942,,source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:n1|duration:8 weeks,brain188 36m control 8w rep4,FASTQ files were extracted using Illumina Casava software v1.8.2.,total RNA extracted from brain,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:brain|age:36 month|treatment:n1|duration:8 weeks,GSM1620942,GSM1620942: brain188 36m control 8w rep4; Danio rerio; RNA Seq,GSM1620942,,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:GSM1620942,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP055573,,,Brain188.fastq.gz,fastq,2159431000.0,43188620.0,GSM1620942 r1,0:50,A:600353952;C:482641833;G:469939355;T:606303730;N:192130,50,,,,600353952,482641833,469939355,606303730,192130,SRX893396,SRS859571,SRA244883,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.91749,,0.16727,,0.69694,,0.53135,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2015-02-27,Adult,Adult,Brain,Nervous System 38445,SRR1821794,SRX893395,SRS859572,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,,brain187 36m control 8w rep3,GSM1620941,,source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:n1|duration:8 weeks,brain187 36m control 8w rep3,FASTQ files were extracted using Illumina Casava software v1.8.2.,total RNA extracted from brain,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:brain|age:36 month|treatment:n1|duration:8 weeks,GSM1620941,GSM1620941: brain187 36m control 8w rep3; Danio rerio; RNA Seq,GSM1620941,,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:GSM1620941,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP055573,,,Brain187.fastq.gz,fastq,2146914450.0,42938289.0,GSM1620941 r1,0:50,A:593471539;C:482978847;G:475357906;T:594986562;N:119596,50,,,,593471539,482978847,475357906,594986562,119596,SRX893395,SRS859572,SRA244883,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.91579,,0.16487,,0.69696,,0.50805,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2015-02-27,Adult,Adult,Brain,Nervous System 38446,SRR1821793,SRX893394,SRS859573,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,,brain186 36m control 8w rep2,GSM1620940,,source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:n1|duration:8 weeks,brain186 36m control 8w rep2,FASTQ files were extracted using Illumina Casava software v1.8.2.,total RNA extracted from brain,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:brain|age:36 month|treatment:n1|duration:8 weeks,GSM1620940,GSM1620940: brain186 36m control 8w rep2; Danio rerio; RNA Seq,GSM1620940,,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:GSM1620940,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP055573,,,Brain186.fastq.gz,fastq,1892437850.0,37848757.0,GSM1620940 r1,0:50,A:529236009;C:421442136;G:411249794;T:530397650;N:112261,50,,,,529236009,421442136,411249794,530397650,112261,SRX893394,SRS859573,SRA244883,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.91541,,0.17265,,0.69394,,0.5234,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2015-02-27,Adult,Adult,Brain,Nervous System 38447,SRR1821792,SRX893393,SRS859574,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,,brain185 36m control 8w rep1,GSM1620939,,source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:n1|duration:8 weeks,brain185 36m control 8w rep1,FASTQ files were extracted using Illumina Casava software v1.8.2.,total RNA extracted from brain,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:brain|age:36 month|treatment:n1|duration:8 weeks,GSM1620939,GSM1620939: brain185 36m control 8w rep1; Danio rerio; RNA Seq,GSM1620939,,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:GSM1620939,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP055573,,,Brain185.fastq.gz,fastq,2412353350.0,48247067.0,GSM1620939 r1,0:50,A:667642370;C:540578365;G:531795577;T:672286916;N:50122,50,,,,667642370,540578365,531795577,672286916,50122,SRX893393,SRS859574,SRA244883,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.9171,,0.15741,,0.6929,,0.52634,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2015-02-27,Adult,Adult,Brain,Nervous System 38448,SRR1821791,SRX893392,SRS859575,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,,brain162 36m control 3w rep3,GSM1620938,,source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:n1|duration:3 weeks,brain162 36m control 3w rep3,FASTQ files were extracted using Illumina Casava software v1.8.2.,total RNA extracted from brain,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:brain|age:36 month|treatment:n1|duration:3 weeks,GSM1620938,GSM1620938: brain162 36m control 3w rep3; Danio rerio; RNA Seq,GSM1620938,,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:GSM1620938,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP055573,,,Brain162.fastq.gz,fastq,2115792900.0,42315858.0,GSM1620938 r1,0:50,A:591284907;C:470346585;G:459440113;T:594665906;N:55389,50,,,,591284907,470346585,459440113,594665906,55389,SRX893392,SRS859575,SRA244883,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.91262,,0.18165,,0.69175,,0.49864,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2015-02-27,Adult,Adult,Brain,Nervous System 38449,SRR1821790,SRX893391,SRS859576,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,,brain161 36m control 3w rep2,GSM1620937,,source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:n1|duration:3 weeks,brain161 36m control 3w rep2,FASTQ files were extracted using Illumina Casava software v1.8.2.,total RNA extracted from brain,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:brain|age:36 month|treatment:n1|duration:3 weeks,GSM1620937,GSM1620937: brain161 36m control 3w rep2; Danio rerio; RNA Seq,GSM1620937,,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:GSM1620937,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP055573,,,Brain161.fastq.gz,fastq,3008253050.0,60165061.0,GSM1620937 r1,0:50,A:837622392;C:671074775;G:660143820;T:839331178;N:80885,50,,,,837622392,671074775,660143820,839331178,80885,SRX893391,SRS859576,SRA244883,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.91262,,0.16992,,0.69497,,0.5073,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2015-02-27,Adult,Adult,Brain,Nervous System 38450,SRR1821789,SRX893390,SRS859577,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,,brain160 36m control 3w rep1,GSM1620936,,source name:total RNA extracted from brain|tissue:brain|age:36 month|treatment:n1|duration:3 weeks,brain160 36m control 3w rep1,FASTQ files were extracted using Illumina Casava software v1.8.2.,total RNA extracted from brain,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:brain|age:36 month|treatment:n1|duration:3 weeks,GSM1620936,GSM1620936: brain160 36m control 3w rep1; Danio rerio; RNA Seq,GSM1620936,,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:GSM1620936,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP055573,,,Brain160.fastq.gz,fastq,2276421850.0,45528437.0,GSM1620936 r1,0:50,A:635790951;C:504584896;G:496496426;T:639505870;N:43707,50,,,,635790951,504584896,496496426,639505870,43707,SRX893390,SRS859577,SRA244883,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.91459,,0.17586,,0.69501,,0.52684,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2015-02-27,Adult,Adult,Brain,Nervous System 38451,SRR1821788,SRX893389,SRS859578,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,,brain184 12m control 8w rep3,GSM1620935,,source name:total RNA extracted from brain|tissue:brain|age:12 month|treatment:n1|duration:8 weeks,brain184 12m control 8w rep3,FASTQ files were extracted using Illumina Casava software v1.8.2.,total RNA extracted from brain,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:brain|age:12 month|treatment:n1|duration:8 weeks,GSM1620935,GSM1620935: brain184 12m control 8w rep3; Danio rerio; RNA Seq,GSM1620935,,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:GSM1620935,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP055573,,,Brain184.fastq.gz,fastq,2278129750.0,45562595.0,GSM1620935 r1,0:50,A:631799307;C:510023581;G:500313528;T:635941275;N:52059,50,,,,631799307,510023581,500313528,635941275,52059,SRX893389,SRS859578,SRA244883,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.91986,,0.1596,,0.69716,,0.51685,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2015-02-27,Adult,Adult,Brain,Nervous System 38452,SRR1821787,SRX893388,SRS859579,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,,brain183 12m control 8w rep2,GSM1620934,,source name:total RNA extracted from brain|tissue:brain|age:12 month|treatment:n1|duration:8 weeks,brain183 12m control 8w rep2,FASTQ files were extracted using Illumina Casava software v1.8.2.,total RNA extracted from brain,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:brain|age:12 month|treatment:n1|duration:8 weeks,GSM1620934,GSM1620934: brain183 12m control 8w rep2; Danio rerio; RNA Seq,GSM1620934,,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:GSM1620934,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP055573,,,Brain183.fastq.gz,fastq,2224353800.0,44487076.0,GSM1620934 r1,0:50,A:618322260;C:496812855;G:486578426;T:622597552;N:42707,50,,,,618322260,496812855,486578426,622597552,42707,SRX893388,SRS859579,SRA244883,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.91707,,0.16186,,0.6981,,0.50647,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2015-02-27,Adult,Adult,Brain,Nervous System 38453,SRR1821786,SRX893387,SRS859580,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,,brain182 12m control 8w rep1,GSM1620933,,source name:total RNA extracted from brain|tissue:brain|age:12 month|treatment:n1|duration:8 weeks,brain182 12m control 8w rep1,FASTQ files were extracted using Illumina Casava software v1.8.2.,total RNA extracted from brain,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:brain|age:12 month|treatment:n1|duration:8 weeks,GSM1620933,GSM1620933: brain182 12m control 8w rep1; Danio rerio; RNA Seq,GSM1620933,,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:GSM1620933,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP055573,,,Brain182.fastq.gz,fastq,2529540100.0,50590802.0,GSM1620933 r1,0:50,A:702082535;C:564419392;G:557247066;T:705743714;N:47393,50,,,,702082535,564419392,557247066,705743714,47393,SRX893387,SRS859580,SRA244883,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.919,,0.1675,,0.69542,,0.51245,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2015-02-27,Adult,Adult,Brain,Nervous System 38454,SRR1821785,SRX893386,SRS859581,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,,brain159 12m control 3w rep3,GSM1620932,,source name:total RNA extracted from brain|tissue:brain|age:12 month|treatment:n1|duration:3 weeks,brain159 12m control 3w rep3,FASTQ files were extracted using Illumina Casava software v1.8.2.,total RNA extracted from brain,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:brain|age:12 month|treatment:n1|duration:3 weeks,GSM1620932,GSM1620932: brain159 12m control 3w rep3; Danio rerio; RNA Seq,GSM1620932,,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:GSM1620932,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP055573,,,Brain159.fastq.gz,fastq,1852400050.0,37048001.0,GSM1620932 r1,0:50,A:516159124;C:413012844;G:403938874;T:519233327;N:55881,50,,,,516159124,413012844,403938874,519233327,55881,SRX893386,SRS859581,SRA244883,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.91641,,0.1728,,0.6911,,0.51585,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2015-02-27,Adult,Adult,Brain,Nervous System 38455,SRR1821784,SRX893385,SRS859582,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,,brain158 12m control 3w rep2,GSM1620931,,source name:total RNA extracted from brain|tissue:brain|age:12 month|treatment:n1|duration:3 weeks,brain158 12m control 3w rep2,FASTQ files were extracted using Illumina Casava software v1.8.2.,total RNA extracted from brain,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:brain|age:12 month|treatment:n1|duration:3 weeks,GSM1620931,GSM1620931: brain158 12m control 3w rep2; Danio rerio; RNA Seq,GSM1620931,,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:GSM1620931,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP055573,,,Brain158.fastq.gz,fastq,1909179250.0,38183585.0,GSM1620931 r1,0:50,A:530445060;C:427180963;G:415243468;T:534710201;N:1599558,50,,,,530445060,427180963,415243468,534710201,1599558,SRX893385,SRS859582,SRA244883,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.91943,,0.17238,,0.69459,,0.50393,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2015-02-27,Adult,Adult,Brain,Nervous System 38456,SRR1821783,SRX893384,SRS859583,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,,brain157 12m control 3w rep1,GSM1620930,,source name:total RNA extracted from brain|tissue:brain|age:12 month|treatment:n1|duration:3 weeks,brain157 12m control 3w rep1,FASTQ files were extracted using Illumina Casava software v1.8.2.,total RNA extracted from brain,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:brain|age:12 month|treatment:n1|duration:3 weeks,GSM1620930,GSM1620930: brain157 12m control 3w rep1; Danio rerio; RNA Seq,GSM1620930,,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:GSM1620930,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP055573,,,Brain157.fastq.gz,fastq,2407579650.0,48151593.0,GSM1620930 r1,0:50,A:670537335;C:536499860;G:527478669;T:672973571;N:90215,50,,,,670537335,536499860,527478669,672973571,90215,SRX893384,SRS859583,SRA244883,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.91661,,0.16668,,0.69538,,0.5014,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2015-02-27,Adult,Adult,Brain,Nervous System 39625,SRR1920171,SRX960487,SRS877482,SRP056356,PRJNA278935,Transcriptome profiling from the brain of male and female zebrafish,GSE67092,Transcriptome Analysis,Genome wide analysis to identify sex specific transcripts in the brain of male and female zebrafish Overall design: Examination of sex specific gene expression in the brain of male vs female zebrafish.,,,,RZB0003 Female,GSM1638735,,source name:Female brain tissue|genotype:Wild type|Sex:female|tissue:Brain,RZB0003 Female,Illumina Casava1.8.2 software used for basecalling. Sequenced reads were uniquely mapped to Zv9 genome using tophat v1.4.1. Mapped reads were filtered of reads duplication quality threshold <= 30 and loaded to Genespring NGS Reads per kilobase per megabase RPKM was calculated and normalized using the DeSeq normalization procedure. Genome build: Zv9 Supplementary files format and content: tab delimited text files include Raw RPKM values and normalized RPKM for each Sample.,Female brain tissue,,Brain from Male and female fish were extracted for RNA extraction. Brain tissues from 5 fish were collected and pooled. RNA Seq library preparation protocol: Total RNA was extracted using TRIzol® Reagent Invitrogen USA. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. The integrity of RNA samples was determined using an Agilent RNA 6000 Nano chip on an Agilent 2100 Bioanalyzer. Samples with RNA Integrity Number RIN value of 8 9 was used for RNA seq library preparation. Messenger RNA sequencing library was prepared using TruSeq total RNA sample preparation kit Illumina; Total RNA sample preparation guide as per the manufacturers instructions with 3 microgram input RNA per library. Quality of RNA seq library was checked following company recommended protocols. RNA sequencing of male and female samples were performed on the Illumina HiSeq2000 Illumina USA one sample per lane machine with single ended 51 bp read length.,,genotype:Wild type|Sex:female|tissue:Brain,GSM1638735,GSM1638735: RZB0003 Female; Danio rerio; RNA Seq,GSM1638735,,1,Brain from Male and female fish were extracted for RNA extraction. Brain tissues from 5 fish were collected and pooled. RNA Seq library preparation protocol: Total RNA was extracted using TRIzol® Reagent Invitrogen USA. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. The integrity of RNA samples was determined using an Agilent RNA 6000 Nano chip on an Agilent 2100 Bioanalyzer. Samples with RNA Integrity Number RIN value of 8 9 was used for RNA seq library preparation. Messenger RNA sequencing library was prepared using TruSeq total RNA sample preparation kit Illumina; Total RNA sample preparation guide as per the manufacturers instructions with 3 microgram input RNA per library. Quality of RNA seq library was checked following company recommended protocols. RNA sequencing of male and female samples were performed on the Illumina HiSeq2000 Illumina USA one sample per lane machine with single ended 51 bp read length.,GEO Accession:GSM1638735,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP056356,,,RZB003_NoIndex_L004_R1_All.fastq.gz,fastq,14531005592.0,191197442.0,GSM1638735 r1,0:76,A:4108884359;C:3166835425;G:3143573307;T:4098665685;N:13046816,76,,,,4108884359,3166835425,3143573307,4098665685,13046816,SRX960487,SRS877482,SRA247878,GEO,"Computational and Systems Biology, Genome Institute of Singapore",1,0.91338,,0.17886,,0.69049,,0.5006,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Singapore,2015-03-20,Undetermined,Undetermined,Brain,Nervous System 39626,SRR1920170,SRX960486,SRS877483,SRP056356,PRJNA278935,Transcriptome profiling from the brain of male and female zebrafish,GSE67092,Transcriptome Analysis,Genome wide analysis to identify sex specific transcripts in the brain of male and female zebrafish Overall design: Examination of sex specific gene expression in the brain of male vs female zebrafish.,,,,RZB0002 Male,GSM1638734,,source name:Male brain tissue|genotype:Wild type|Sex:male|tissue:Brain,RZB0002 Male,Illumina Casava1.8.2 software used for basecalling. Sequenced reads were uniquely mapped to Zv9 genome using tophat v1.4.1. Mapped reads were filtered of reads duplication quality threshold <= 30 and loaded to Genespring NGS Reads per kilobase per megabase RPKM was calculated and normalized using the DeSeq normalization procedure. Genome build: Zv9 Supplementary files format and content: tab delimited text files include Raw RPKM values and normalized RPKM for each Sample.,Male brain tissue,,Brain from Male and female fish were extracted for RNA extraction. Brain tissues from 5 fish were collected and pooled. RNA Seq library preparation protocol: Total RNA was extracted using TRIzol® Reagent Invitrogen USA. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. The integrity of RNA samples was determined using an Agilent RNA 6000 Nano chip on an Agilent 2100 Bioanalyzer. Samples with RNA Integrity Number RIN value of 8 9 was used for RNA seq library preparation. Messenger RNA sequencing library was prepared using TruSeq total RNA sample preparation kit Illumina; Total RNA sample preparation guide as per the manufacturers instructions with 3 microgram input RNA per library. Quality of RNA seq library was checked following company recommended protocols. RNA sequencing of male and female samples were performed on the Illumina HiSeq2000 Illumina USA one sample per lane machine with single ended 51 bp read length.,,genotype:Wild type|Sex:male|tissue:Brain,GSM1638734,GSM1638734: RZB0002 Male; Danio rerio; RNA Seq,GSM1638734,,1,Brain from Male and female fish were extracted for RNA extraction. Brain tissues from 5 fish were collected and pooled. RNA Seq library preparation protocol: Total RNA was extracted using TRIzol® Reagent Invitrogen USA. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. The integrity of RNA samples was determined using an Agilent RNA 6000 Nano chip on an Agilent 2100 Bioanalyzer. Samples with RNA Integrity Number RIN value of 8 9 was used for RNA seq library preparation. Messenger RNA sequencing library was prepared using TruSeq total RNA sample preparation kit Illumina; Total RNA sample preparation guide as per the manufacturers instructions with 3 microgram input RNA per library. Quality of RNA seq library was checked following company recommended protocols. RNA sequencing of male and female samples were performed on the Illumina HiSeq2000 Illumina USA one sample per lane machine with single ended 51 bp read length.,GEO Accession:GSM1638734,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP056356,,,RZB002_NoIndex_L001_R1_All.fastq.gz,fastq,14711238148.0,193568923.0,GSM1638734 r1,0:76,A:4154125162;C:3219757523;G:3187842434;T:4138123659;N:11389370,76,,,,4154125162,3219757523,3187842434,4138123659,11389370,SRX960486,SRS877483,SRA247878,GEO,"Computational and Systems Biology, Genome Institute of Singapore",1,0.91063,,0.20427,,0.70183,,0.50769,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Singapore,2015-03-20,Undetermined,Undetermined,Brain,Nervous System 40049,SRR2750996,SRX1362066,SRS1125457,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 brain 117,GSM1915502,,source name:total RNA extracted from brain|strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:brain,NH FLI brain 117,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 brain,,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:brain,GSM1915502,GSM1915502: NH FLI brain 117; Danio rerio; RNA Seq,GSM1915502,,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:GSM1915502,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,brain_42m_DR117.fq.gz,fastq,3406050150.0,68121003.0,GSM1915502 r1,0:50,A:943199406;C:761631021;G:756228458;T:944514461;N:476804,50,,,,943199406,761631021,756228458,944514461,476804,SRX1362066,SRS1125457,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.92465,,0.18996,,0.70396,,0.51498,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2015-10-21,Adult,Adult,Brain,Nervous System 40050,SRR2750995,SRX1362065,SRS1125455,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 brain 116,GSM1915501,,source name:total RNA extracted from brain|strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:brain,NH FLI brain 116,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 brain,,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:brain,GSM1915501,GSM1915501: NH FLI brain 116; Danio rerio; RNA Seq,GSM1915501,,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:GSM1915501,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,brain_42m_DR116.fq.gz,fastq,2611587100.0,52231742.0,GSM1915501 r1,0:50,A:723539911;C:589201526;G:571205645;T:727290669;N:349349,50,,,,723539911,589201526,571205645,727290669,349349,SRX1362065,SRS1125455,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.92626,,0.19046,,0.70538,,0.49219,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2015-10-21,Adult,Adult,Brain,Nervous System 40051,SRR2750994,SRX1362064,SRS1125407,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 brain 113,GSM1915500,,source name:total RNA extracted from brain|strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:brain,NH FLI brain 113,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 brain,,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:brain,GSM1915500,GSM1915500: NH FLI brain 113; Danio rerio; RNA Seq,GSM1915500,,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:GSM1915500,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,brain_42m_DR113.fq.gz,fastq,2491364900.0,49827298.0,GSM1915500 r1,0:50,A:689721492;C:559218894;G:549684395;T:692580806;N:159313,50,,,,689721492,559218894,549684395,692580806,159313,SRX1362064,SRS1125407,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.92834,,0.1784,,0.70193,,0.52293,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2015-10-21,Adult,Adult,Brain,Nervous System 40052,SRR2750993,SRX1362063,SRS1125456,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 brain 112,GSM1915499,,source name:total RNA extracted from brain|strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:brain,NH FLI brain 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 brain,,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:brain,GSM1915499,GSM1915499: NH FLI brain 112; Danio rerio; RNA Seq,GSM1915499,,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:GSM1915499,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,brain_42m_DR112.fq.gz,fastq,2551111100.0,51022222.0,GSM1915499 r1,0:50,A:715464906;C:564236701;G:552616854;T:718233491;N:559148,50,,,,715464906,564236701,552616854,718233491,559148,SRX1362063,SRS1125456,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.92758,,0.1859,,0.70802,,0.52244,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2015-10-21,Adult,Adult,Brain,Nervous System 40053,SRR2750992,SRX1362062,SRS1125459,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 brain 111,GSM1915498,,source name:total RNA extracted from brain|strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:brain,NH FLI brain 111,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 brain,,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:brain,GSM1915498,GSM1915498: NH FLI brain 111; Danio rerio; RNA Seq,GSM1915498,,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:GSM1915498,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,brain_42m_DR111.fq.gz,fastq,2457310750.0,49146215.0,GSM1915498 r1,0:50,A:681859455;C:551379777;G:537063740;T:686575784;N:431994,50,,,,681859455,551379777,537063740,686575784,431994,SRX1362062,SRS1125459,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.92475,,0.18969,,0.70177,,0.52316,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2015-10-21,Adult,Adult,Brain,Nervous System 40054,SRR2750991,SRX1362061,SRS1125462,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 brain 149,GSM1915497,,source name:total RNA extracted from brain|strain:AB JxTu Tgpu.1:GFP|age:36 month|age category:old 1|tissue:brain,NH FLI brain 149,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 brain,,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:brain,GSM1915497,GSM1915497: NH FLI brain 149; Danio rerio; RNA Seq,GSM1915497,,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:GSM1915497,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,brain_36m_DR149.fq.gz,fastq,3266609800.0,65332196.0,GSM1915497 r1,0:50,A:910236190;C:730082959;G:713296931;T:912495297;N:498423,50,,,,910236190,730082959,713296931,912495297,498423,SRX1362061,SRS1125462,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.92165,,0.17163,,0.70138,,0.5021,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2015-10-21,Adult,Adult,Brain,Nervous System 40055,SRR2750990,SRX1362060,SRS1125460,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 brain 148,GSM1915496,,source name:total RNA extracted from brain|strain:AB JxTu Tgpu.1:GFP|age:36 month|age category:old 1|tissue:brain,NH FLI brain 148,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 brain,,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:brain,GSM1915496,GSM1915496: NH FLI brain 148; Danio rerio; RNA Seq,GSM1915496,,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:GSM1915496,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,brain_36m_DR148.fq.gz,fastq,2464883900.0,49297678.0,GSM1915496 r1,0:50,A:686732382;C:549891282;G:537616130;T:690342039;N:302067,50,,,,686732382,549891282,537616130,690342039,302067,SRX1362060,SRS1125460,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.92312,,0.17867,,0.70297,,0.51462,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2015-10-21,Adult,Adult,Brain,Nervous System 40056,SRR2750989,SRX1362059,SRS1125461,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 brain 147,GSM1915495,,source name:total RNA extracted from brain|strain:AB JxTu Tgpu.1:GFP|age:36 month|age category:old 1|tissue:brain,NH FLI brain 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 brain,,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:brain,GSM1915495,GSM1915495: NH FLI brain 147; Danio rerio; RNA Seq,GSM1915495,,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:GSM1915495,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,brain_36m_DR147.fq.gz,fastq,2474644500.0,49492890.0,GSM1915495 r1,0:50,A:685124761;C:555034624;G:544745611;T:689478260;N:261244,50,,,,685124761,555034624,544745611,689478260,261244,SRX1362059,SRS1125461,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.92436,,0.18206,,0.69617,,0.49333,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2015-10-21,Adult,Adult,Brain,Nervous System 40057,SRR2750988,SRX1362058,SRS1125463,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 brain 146,GSM1915494,,source name:total RNA extracted from brain|strain:AB JxTu Tgpu.1:GFP|age:36 month|age category:old 1|tissue:brain,NH FLI brain 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 brain,,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:brain,GSM1915494,GSM1915494: NH FLI brain 146; Danio rerio; RNA Seq,GSM1915494,,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:GSM1915494,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,brain_36m_DR146.fq.gz,fastq,2597663300.0,51953266.0,GSM1915494 r1,0:50,A:716263646;C:586797961;G:575830224;T:718269464;N:502005,50,,,,716263646,586797961,575830224,718269464,502005,SRX1362058,SRS1125463,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.92305,,0.18336,,0.69718,,0.49808,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2015-10-21,Adult,Adult,Brain,Nervous System 40058,SRR2750987,SRX1362057,SRS1125465,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 brain 145,GSM1915493,,source name:total RNA extracted from brain|strain:AB JxTu Tgpu.1:GFP|age:36 month|age category:old 1|tissue:brain,NH FLI brain 145,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 brain,,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:brain,GSM1915493,GSM1915493: NH FLI brain 145; Danio rerio; RNA Seq,GSM1915493,,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:GSM1915493,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,brain_36m_DR145.fq.gz,fastq,2425454500.0,48509090.0,GSM1915493 r1,0:50,A:669150954;C:547473225;G:539693976;T:668621375;N:514970,50,,,,669150954,547473225,539693976,668621375,514970,SRX1362057,SRS1125465,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.92429,,0.17339,,0.69942,,0.5091,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2015-10-21,Adult,Adult,Brain,Nervous System 40059,SRR2750986,SRX1362056,SRS1125464,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 brain 136,GSM1915492,,source name:total RNA extracted from brain|strain:AB JxTu|age:24 month|age category: |tissue:brain,NH FLI brain 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 brain,,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:brain,GSM1915492,GSM1915492: NH FLI brain 136; Danio rerio; RNA Seq,GSM1915492,,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:GSM1915492,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,brain_24m_DR136.fq.gz,fastq,3126615200.0,62532304.0,GSM1915492 r1,0:50,A:862834835;C:707795697;G:685293451;T:870533222;N:157995,50,,,,862834835,707795697,685293451,870533222,157995,SRX1362056,SRS1125464,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.93145,,0.17791,,0.68842,,0.50923,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2015-10-21,Adult,Adult,Brain,Nervous System 40060,SRR2750985,SRX1362055,SRS1125468,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 brain 135,GSM1915491,,source name:total RNA extracted from brain|strain:AB JxTu|age:24 month|age category: |tissue:brain,NH FLI brain 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 brain,,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:brain,GSM1915491,GSM1915491: NH FLI brain 135; Danio rerio; RNA Seq,GSM1915491,,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:GSM1915491,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,brain_24m_DR135.fq.gz,fastq,2930861000.0,58617220.0,GSM1915491 r1,0:50,A:811764434;C:655387329;G:652457326;T:810896969;N:354942,50,,,,811764434,655387329,652457326,810896969,354942,SRX1362055,SRS1125468,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.93193,,0.18175,,0.7108,,0.51807,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2015-10-21,Adult,Adult,Brain,Nervous System 40061,SRR2750984,SRX1362054,SRS1125406,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 brain 134,GSM1915490,,source name:total RNA extracted from brain|strain:AB JxTu|age:24 month|age category: |tissue:brain,NH FLI brain 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 brain,,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:brain,GSM1915490,GSM1915490: NH FLI brain 134; Danio rerio; RNA Seq,GSM1915490,,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:GSM1915490,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,brain_24m_DR134.fq.gz,fastq,2763753000.0,55275060.0,GSM1915490 r1,0:50,A:768004531;C:617158156;G:612876215;T:765618799;N:95299,50,,,,768004531,617158156,612876215,765618799,95299,SRX1362054,SRS1125406,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.93138,,0.18088,,0.70358,,0.51438,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2015-10-21,Adult,Adult,Brain,Nervous System 40062,SRR2750983,SRX1362053,SRS1125466,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 brain 133,GSM1915489,,source name:total RNA extracted from brain|strain:AB JxTu|age:24 month|age category: |tissue:brain,NH FLI brain 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 brain,,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:brain,GSM1915489,GSM1915489: NH FLI brain 133; Danio rerio; RNA Seq,GSM1915489,,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:GSM1915489,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,brain_24m_DR133.fq.gz,fastq,2711487000.0,54229740.0,GSM1915489 r1,0:50,A:753048714;C:605974497;G:595850286;T:756230644;N:382859,50,,,,753048714,605974497,595850286,756230644,382859,SRX1362053,SRS1125466,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.93713,,0.17806,,0.70512,,0.5315,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2015-10-21,Adult,Adult,Brain,Nervous System 40063,SRR2750982,SRX1362052,SRS1125467,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 brain 132,GSM1915488,,source name:total RNA extracted from brain|strain:AB JxTu|age:24 month|age category: |tissue:brain,NH FLI brain 132,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 brain,,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:brain,GSM1915488,GSM1915488: NH FLI brain 132; Danio rerio; RNA Seq,GSM1915488,,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:GSM1915488,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,brain_24m_DR132.fq.gz,fastq,2431155350.0,48623107.0,GSM1915488 r1,0:50,A:673834712;C:548795822;G:530868509;T:677188005;N:468302,50,,,,673834712,548795822,530868509,677188005,468302,SRX1362052,SRS1125467,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.92967,,0.18591,,0.69787,,0.498,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2015-10-21,Adult,Adult,Brain,Nervous System 40064,SRR2750981,SRX1362051,SRS1125470,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 brain 124,GSM1915487,,source name:total RNA extracted from brain|strain:AB JxTu Tgflk:mCherry|age:12 month|age category: |tissue:brain,NH FLI brain 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 brain,,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:brain,GSM1915487,GSM1915487: NH FLI brain 124; Danio rerio; RNA Seq,GSM1915487,,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:GSM1915487,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,brain_12m_DR124.fq.gz,fastq,2610060550.0,52201211.0,GSM1915487 r1,0:50,A:725078902;C:586028252;G:571130665;T:727698335;N:124396,50,,,,725078902,586028252,571130665,727698335,124396,SRX1362051,SRS1125470,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.92145,,0.18055,,0.7063,,0.49931,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2015-10-21,Adult,Adult,Brain,Nervous System 40065,SRR2750980,SRX1362050,SRS1125469,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 brain 122,GSM1915486,,source name:total RNA extracted from brain|strain:AB JxTu Tgflk:mCherry|age:12 month|age category: |tissue:brain,NH FLI brain 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 brain,,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:brain,GSM1915486,GSM1915486: NH FLI brain 122; Danio rerio; RNA Seq,GSM1915486,,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:GSM1915486,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,brain_12m_DR122.fq.gz,fastq,4176155600.0,83523112.0,GSM1915486 r1,0:50,A:1163933913;C:938439453;G:904273013;T:1167599992;N:1909229,50,,,,1163933913,938439453,904273013,1167599992,1909229,SRX1362050,SRS1125469,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.91827,,0.17458,,0.7208,,0.52607,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2015-10-21,Adult,Adult,Brain,Nervous System 40066,SRR2750979,SRX1362049,SRS1125471,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 brain 121,GSM1915485,,source name:total RNA extracted from brain|strain:AB JxTu Tgflk:mCherry|age:12 month|age category: |tissue:brain,NH FLI brain 121,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 brain,,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:brain,GSM1915485,GSM1915485: NH FLI brain 121; Danio rerio; RNA Seq,GSM1915485,,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:GSM1915485,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,brain_12m_DR121.fq.gz,fastq,2365406900.0,47308138.0,GSM1915485 r1,0:50,A:658768973;C:526129795;G:518696418;T:661664238;N:147476,50,,,,658768973,526129795,518696418,661664238,147476,SRX1362049,SRS1125471,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.9278,,0.17501,,0.70682,,0.50725,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2015-10-21,Adult,Adult,Brain,Nervous System 40067,SRR2750978,SRX1362048,SRS1125473,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 brain 120,GSM1915484,,source name:total RNA extracted from brain|strain:AB JxTu Tgflk:mCherry|age:12 month|age category: |tissue:brain,NH FLI brain 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 brain,,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:brain,GSM1915484,GSM1915484: NH FLI brain 120; Danio rerio; RNA Seq,GSM1915484,,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:GSM1915484,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,brain_12m_DR120.fq.gz,fastq,2814312950.0,56286259.0,GSM1915484 r1,0:50,A:789301611;C:623070571;G:607867048;T:793389268;N:684452,50,,,,789301611,623070571,607867048,793389268,684452,SRX1362048,SRS1125473,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.92494,,0.18932,,0.70406,,0.52384,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2015-10-21,Adult,Adult,Brain,Nervous System 40068,SRR2750977,SRX1362047,SRS1125472,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 brain 119,GSM1915483,,source name:total RNA extracted from brain|strain:AB JxTu Tgflk:mCherry|age:12 month|age category: |tissue:brain,NH FLI brain 119,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 brain,,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:brain,GSM1915483,GSM1915483: NH FLI brain 119; Danio rerio; RNA Seq,GSM1915483,,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:GSM1915483,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,brain_12m_DR119.fq.gz,fastq,2649286550.0,52985731.0,GSM1915483 r1,0:50,A:736478890;C:593776908;G:582885086;T:735865205;N:280461,50,,,,736478890,593776908,582885086,735865205,280461,SRX1362047,SRS1125472,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.92553,,0.16885,,0.70595,,0.52454,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2015-10-21,Adult,Adult,Brain,Nervous System 40069,SRR2750976,SRX1362046,SRS1125474,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 brain 99+100,GSM1915482,,source name:total RNA extracted from brain|strain:AB JxTu|age:6 month|age category:young|tissue:brain,NH FLI brain 99+100,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 brain,,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:brain,GSM1915482,GSM1915482: NH FLI brain 99+100; Danio rerio; RNA Seq,GSM1915482,,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:GSM1915482,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,brain_6m_DR99DR100.fq.gz,fastq,2944591900.0,58891838.0,GSM1915482 r1,0:50,A:809123579;C:666281689;G:661175059;T:807800761;N:210812,50,,,,809123579,666281689,661175059,807800761,210812,SRX1362046,SRS1125474,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.93377,,0.17733,,0.69587,,0.48159,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2015-10-21,Adult,Adult,Brain,Nervous System 40070,SRR2750975,SRX1362045,SRS1125475,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 brain 97+98,GSM1915481,,source name:total RNA extracted from brain|strain:AB JxTu|age:6 month|age category:young|tissue:brain,NH FLI brain 97+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 brain,,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:brain,GSM1915481,GSM1915481: NH FLI brain 97+98; Danio rerio; RNA Seq,GSM1915481,,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:GSM1915481,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,brain_6m_DR97DR98.fq.gz,fastq,2470909450.0,49418189.0,GSM1915481 r1,0:50,A:680518660;C:559579355;G:549977093;T:680513978;N:320364,50,,,,680518660,559579355,549977093,680513978,320364,SRX1362045,SRS1125475,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.93007,,0.17968,,0.70441,,0.50437,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2015-10-21,Adult,Adult,Brain,Nervous System 40071,SRR2750974,SRX1362044,SRS1125476,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 brain 95+96,GSM1915480,,source name:total RNA extracted from brain|strain:AB JxTu|age:6 month|age category:young|tissue:brain,NH FLI brain 95+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 brain,,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:brain,GSM1915480,GSM1915480: NH FLI brain 95+96; Danio rerio; RNA Seq,GSM1915480,,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:GSM1915480,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,brain_6m_DR95DR96.fq.gz,fastq,2321660700.0,46433214.0,GSM1915480 r1,0:50,A:639876205;C:526478329;G:511193842;T:643800112;N:312212,50,,,,639876205,526478329,511193842,643800112,312212,SRX1362044,SRS1125476,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.93035,,0.17563,,0.70532,,0.49124,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2015-10-21,Adult,Adult,Brain,Nervous System 40072,SRR2750973,SRX1362043,SRS1125477,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 brain 103+104,GSM1915479,,source name:total RNA extracted from brain|strain:AB JxTu|age:6 month|age category:young|tissue:brain,NH FLI brain 103+104,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 brain,,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:brain,GSM1915479,GSM1915479: NH FLI brain 103+104; Danio rerio; RNA Seq,GSM1915479,,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:GSM1915479,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,brain_6m_DR103DR104.fq.gz,fastq,2724600950.0,54492019.0,GSM1915479 r1,0:50,A:749712664;C:618586700;G:601819865;T:754300495;N:181226,50,,,,749712664,618586700,601819865,754300495,181226,SRX1362043,SRS1125477,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.92924,,0.17223,,0.69998,,0.50685,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2015-10-21,Adult,Adult,Brain,Nervous System 40073,SRR2750972,SRX1362042,SRS1125478,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 brain 101+102,GSM1915478,,source name:total RNA extracted from brain|strain:AB JxTu|age:6 month|age category:young|tissue:brain,NH FLI brain 101+102,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 brain,,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:brain,GSM1915478,GSM1915478: NH FLI brain 101+102; Danio rerio; RNA Seq,GSM1915478,,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:GSM1915478,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,brain_6m_DR101DR102.fq.gz,fastq,2489983500.0,49799670.0,GSM1915478 r1,0:50,A:690756776;C:557024748;G:546528174;T:695481491;N:192311,50,,,,690756776,557024748,546528174,695481491,192311,SRX1362042,SRS1125478,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.93192,,0.18151,,0.6956,,0.50256,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Germany,2015-10-21,Adult,Adult,Brain,Nervous System