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 43758,SRR6072798,SRX3214272,SRS2539011,SRP118819,PRJNA412050,Integrative analysis of transcriptional and DNA methylation changes associated with PCB126 exposure in adult zebrafish Danio rerio,GSE104221,Other,The aryl hydrocarbon receptor AHR is a ligand activated transcription factor well known for mediating the toxicity of environmental chemicals such as polychlorinated biphenyls PCBs and polyaromatic hydrocarbons PAHs. There is extensive knowledge on the range of target genes regulated by AHR ligands. However there is limited information on the effect of AHR ligands on DNA methylation. The objective of this study is to investigate genome wide changes in DNA methylation and gene expression patterns in response to PCB126 exposure. Adult zebrafish were exposed to 10 nM PCB126 for 24 hours waterborne exposure and were reared in clean water for xxx days before tissue sampling. DNA methylation and transcriptional changes in the liver and brain tissues were quantified by Reduced Representation Bisulfite Sequencing RRBS and RNAseq respectively. RRBS analysis revealed DNA hypomethylation in response to PCB exposure in both liver and brain tissues. We observed 482 and 476 differentially methylated regions DMRs in the liver and brain tissues respectively. Most of the DMRs are located more than 20 kilobases upstream of the transcriptional start sites. RNAseq results from the liver revealed differential expression of genes related to xenobiotic metabolism oxidative stress and carbohydrate metabolism in response to PCB exposure. In the brain PCB exposure altered the expression of genes involved in myelination and glutamate signaling. Our results suggest that there is very little correlation between DNA methylation and gene expression patterns among the differentially expressed genes DEGs. We are currently investigating the relationship between DMRs and DEGs. Overall design: Two different tissues Liver and brain from PCB126 and DMSO exposed zebrafish were analyzed for DNA methylation and gene expression using RRBS and RNAseq respectively. Four biological replicates per treatment were analyzed n=4 individual fish.,,pubmed:29686887,,PCB126 BRAIN4 RNA Seq,GSM2792798,,tissue:brain|treatment:PCB126|life history stage:Adult,PCB126 BRAIN4 RNA Seq,Enhanced RRBS data was processed by aligning the reads to the bisulfite converted genome using Bismark. CpG methylation calls were extracted from Bismark aligned bam files using MethylKit. Differential methylation analysis was carried out by SLIM method using methylKit RNAseq data was pre processed and aligned to the genome using STAR aligner and HTSeqcount was used to obtain mapped read counts Genome build: GRCz10 Supplementary files format and content: text files for RNAseq include mapped read counts; text files for ERRBS include CpG methylation calls.,brain,Adult zebrafish were exposed to either PCB126 or DMSO via waterborne exposure for xxx hours. post the exposure period fish were reared in clean water for 7 days before sampling the tissues.,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,,treatment:PCB126|life history stage:Adult,GSM2792798,GSM2792798: PCB126 BRAIN4 RNA Seq; Danio rerio; RNA Seq,GSM2792798,,1,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,GEO Accession:GSM2792798,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP118819,,,PB4_S16_L002_R1_001.fastq.gz,fastq,1375628508.0,26973108.0,GSM2792798 r1,0:51 1:0,A:389260936;C:298336750;G:285290157;T:402727589;N:13076,51,0,,,389260936,298336750,285290157,402727589,13076,SRX3214272,SRS2539011,SRA612796,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.90102,,0.20673,,0.69152,,0.51941,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2017-09-25,Adult,Adult,Brain,Nervous System 43759,SRR6072797,SRX3214271,SRS2539012,SRP118819,PRJNA412050,Integrative analysis of transcriptional and DNA methylation changes associated with PCB126 exposure in adult zebrafish Danio rerio,GSE104221,Other,The aryl hydrocarbon receptor AHR is a ligand activated transcription factor well known for mediating the toxicity of environmental chemicals such as polychlorinated biphenyls PCBs and polyaromatic hydrocarbons PAHs. There is extensive knowledge on the range of target genes regulated by AHR ligands. However there is limited information on the effect of AHR ligands on DNA methylation. The objective of this study is to investigate genome wide changes in DNA methylation and gene expression patterns in response to PCB126 exposure. Adult zebrafish were exposed to 10 nM PCB126 for 24 hours waterborne exposure and were reared in clean water for xxx days before tissue sampling. DNA methylation and transcriptional changes in the liver and brain tissues were quantified by Reduced Representation Bisulfite Sequencing RRBS and RNAseq respectively. RRBS analysis revealed DNA hypomethylation in response to PCB exposure in both liver and brain tissues. We observed 482 and 476 differentially methylated regions DMRs in the liver and brain tissues respectively. Most of the DMRs are located more than 20 kilobases upstream of the transcriptional start sites. RNAseq results from the liver revealed differential expression of genes related to xenobiotic metabolism oxidative stress and carbohydrate metabolism in response to PCB exposure. In the brain PCB exposure altered the expression of genes involved in myelination and glutamate signaling. Our results suggest that there is very little correlation between DNA methylation and gene expression patterns among the differentially expressed genes DEGs. We are currently investigating the relationship between DMRs and DEGs. Overall design: Two different tissues Liver and brain from PCB126 and DMSO exposed zebrafish were analyzed for DNA methylation and gene expression using RRBS and RNAseq respectively. Four biological replicates per treatment were analyzed n=4 individual fish.,,pubmed:29686887,,PCB126 BRAIN3 RNA Seq,GSM2792797,,tissue:brain|treatment:PCB126|life history stage:Adult,PCB126 BRAIN3 RNA Seq,Enhanced RRBS data was processed by aligning the reads to the bisulfite converted genome using Bismark. CpG methylation calls were extracted from Bismark aligned bam files using MethylKit. Differential methylation analysis was carried out by SLIM method using methylKit RNAseq data was pre processed and aligned to the genome using STAR aligner and HTSeqcount was used to obtain mapped read counts Genome build: GRCz10 Supplementary files format and content: text files for RNAseq include mapped read counts; text files for ERRBS include CpG methylation calls.,brain,Adult zebrafish were exposed to either PCB126 or DMSO via waterborne exposure for xxx hours. post the exposure period fish were reared in clean water for 7 days before sampling the tissues.,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,,treatment:PCB126|life history stage:Adult,GSM2792797,GSM2792797: PCB126 BRAIN3 RNA Seq; Danio rerio; RNA Seq,GSM2792797,,1,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,GEO Accession:GSM2792797,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP118819,,,PB3_S15_L002_R1_001.fastq.gz,fastq,1534214028.0,30082628.0,GSM2792797 r1,0:51 1:0,A:434098364;C:333114785;G:318943720;T:448043305;N:13854,51,0,,,434098364,333114785,318943720,448043305,13854,SRX3214271,SRS2539012,SRA612796,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.88591,,0.19161,,0.67967,,0.53267,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2017-09-25,Adult,Adult,Brain,Nervous System 43760,SRR6072796,SRX3214270,SRS2539009,SRP118819,PRJNA412050,Integrative analysis of transcriptional and DNA methylation changes associated with PCB126 exposure in adult zebrafish Danio rerio,GSE104221,Other,The aryl hydrocarbon receptor AHR is a ligand activated transcription factor well known for mediating the toxicity of environmental chemicals such as polychlorinated biphenyls PCBs and polyaromatic hydrocarbons PAHs. There is extensive knowledge on the range of target genes regulated by AHR ligands. However there is limited information on the effect of AHR ligands on DNA methylation. The objective of this study is to investigate genome wide changes in DNA methylation and gene expression patterns in response to PCB126 exposure. Adult zebrafish were exposed to 10 nM PCB126 for 24 hours waterborne exposure and were reared in clean water for xxx days before tissue sampling. DNA methylation and transcriptional changes in the liver and brain tissues were quantified by Reduced Representation Bisulfite Sequencing RRBS and RNAseq respectively. RRBS analysis revealed DNA hypomethylation in response to PCB exposure in both liver and brain tissues. We observed 482 and 476 differentially methylated regions DMRs in the liver and brain tissues respectively. Most of the DMRs are located more than 20 kilobases upstream of the transcriptional start sites. RNAseq results from the liver revealed differential expression of genes related to xenobiotic metabolism oxidative stress and carbohydrate metabolism in response to PCB exposure. In the brain PCB exposure altered the expression of genes involved in myelination and glutamate signaling. Our results suggest that there is very little correlation between DNA methylation and gene expression patterns among the differentially expressed genes DEGs. We are currently investigating the relationship between DMRs and DEGs. Overall design: Two different tissues Liver and brain from PCB126 and DMSO exposed zebrafish were analyzed for DNA methylation and gene expression using RRBS and RNAseq respectively. Four biological replicates per treatment were analyzed n=4 individual fish.,,pubmed:29686887,,PCB126 BRAIN2 RNA Seq,GSM2792796,,tissue:brain|treatment:PCB126|life history stage:Adult,PCB126 BRAIN2 RNA Seq,Enhanced RRBS data was processed by aligning the reads to the bisulfite converted genome using Bismark. CpG methylation calls were extracted from Bismark aligned bam files using MethylKit. Differential methylation analysis was carried out by SLIM method using methylKit RNAseq data was pre processed and aligned to the genome using STAR aligner and HTSeqcount was used to obtain mapped read counts Genome build: GRCz10 Supplementary files format and content: text files for RNAseq include mapped read counts; text files for ERRBS include CpG methylation calls.,brain,Adult zebrafish were exposed to either PCB126 or DMSO via waterborne exposure for xxx hours. post the exposure period fish were reared in clean water for 7 days before sampling the tissues.,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,,treatment:PCB126|life history stage:Adult,GSM2792796,GSM2792796: PCB126 BRAIN2 RNA Seq; Danio rerio; RNA Seq,GSM2792796,,1,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,GEO Accession:GSM2792796,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP118819,,,PB2_S14_L002_R1_001.fastq.gz,fastq,1492641276.0,29267476.0,GSM2792796 r1,0:51 1:0,A:419506485;C:327077186;G:314622527;T:431420803;N:14275,51,0,,,419506485,327077186,314622527,431420803,14275,SRX3214270,SRS2539009,SRA612796,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.89327,,0.18282,,0.68777,,0.53375,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2017-09-25,Adult,Adult,Brain,Nervous System 43761,SRR6072795,SRX3214269,SRS2539010,SRP118819,PRJNA412050,Integrative analysis of transcriptional and DNA methylation changes associated with PCB126 exposure in adult zebrafish Danio rerio,GSE104221,Other,The aryl hydrocarbon receptor AHR is a ligand activated transcription factor well known for mediating the toxicity of environmental chemicals such as polychlorinated biphenyls PCBs and polyaromatic hydrocarbons PAHs. There is extensive knowledge on the range of target genes regulated by AHR ligands. However there is limited information on the effect of AHR ligands on DNA methylation. The objective of this study is to investigate genome wide changes in DNA methylation and gene expression patterns in response to PCB126 exposure. Adult zebrafish were exposed to 10 nM PCB126 for 24 hours waterborne exposure and were reared in clean water for xxx days before tissue sampling. DNA methylation and transcriptional changes in the liver and brain tissues were quantified by Reduced Representation Bisulfite Sequencing RRBS and RNAseq respectively. RRBS analysis revealed DNA hypomethylation in response to PCB exposure in both liver and brain tissues. We observed 482 and 476 differentially methylated regions DMRs in the liver and brain tissues respectively. Most of the DMRs are located more than 20 kilobases upstream of the transcriptional start sites. RNAseq results from the liver revealed differential expression of genes related to xenobiotic metabolism oxidative stress and carbohydrate metabolism in response to PCB exposure. In the brain PCB exposure altered the expression of genes involved in myelination and glutamate signaling. Our results suggest that there is very little correlation between DNA methylation and gene expression patterns among the differentially expressed genes DEGs. We are currently investigating the relationship between DMRs and DEGs. Overall design: Two different tissues Liver and brain from PCB126 and DMSO exposed zebrafish were analyzed for DNA methylation and gene expression using RRBS and RNAseq respectively. Four biological replicates per treatment were analyzed n=4 individual fish.,,pubmed:29686887,,PCB126 BRAIN1 RNA Seq,GSM2792795,,tissue:brain|treatment:PCB126|life history stage:Adult,PCB126 BRAIN1 RNA Seq,Enhanced RRBS data was processed by aligning the reads to the bisulfite converted genome using Bismark. CpG methylation calls were extracted from Bismark aligned bam files using MethylKit. Differential methylation analysis was carried out by SLIM method using methylKit RNAseq data was pre processed and aligned to the genome using STAR aligner and HTSeqcount was used to obtain mapped read counts Genome build: GRCz10 Supplementary files format and content: text files for RNAseq include mapped read counts; text files for ERRBS include CpG methylation calls.,brain,Adult zebrafish were exposed to either PCB126 or DMSO via waterborne exposure for xxx hours. post the exposure period fish were reared in clean water for 7 days before sampling the tissues.,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,,treatment:PCB126|life history stage:Adult,GSM2792795,GSM2792795: PCB126 BRAIN1 RNA Seq; Danio rerio; RNA Seq,GSM2792795,,1,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,GEO Accession:GSM2792795,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP118819,,,PB1_S13_L002_R1_001.fastq.gz,fastq,1540239576.0,30200776.0,GSM2792795 r1,0:51 1:0,A:425532690;C:346041208;G:332010797;T:436640179;N:14702,51,0,,,425532690,346041208,332010797,436640179,14702,SRX3214269,SRS2539010,SRA612796,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.8846,,0.14495,,0.67142,,0.51907,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2017-09-25,Adult,Adult,Brain,Nervous System 43762,SRR6072794,SRX3214268,SRS2539008,SRP118819,PRJNA412050,Integrative analysis of transcriptional and DNA methylation changes associated with PCB126 exposure in adult zebrafish Danio rerio,GSE104221,Other,The aryl hydrocarbon receptor AHR is a ligand activated transcription factor well known for mediating the toxicity of environmental chemicals such as polychlorinated biphenyls PCBs and polyaromatic hydrocarbons PAHs. There is extensive knowledge on the range of target genes regulated by AHR ligands. However there is limited information on the effect of AHR ligands on DNA methylation. The objective of this study is to investigate genome wide changes in DNA methylation and gene expression patterns in response to PCB126 exposure. Adult zebrafish were exposed to 10 nM PCB126 for 24 hours waterborne exposure and were reared in clean water for xxx days before tissue sampling. DNA methylation and transcriptional changes in the liver and brain tissues were quantified by Reduced Representation Bisulfite Sequencing RRBS and RNAseq respectively. RRBS analysis revealed DNA hypomethylation in response to PCB exposure in both liver and brain tissues. We observed 482 and 476 differentially methylated regions DMRs in the liver and brain tissues respectively. Most of the DMRs are located more than 20 kilobases upstream of the transcriptional start sites. RNAseq results from the liver revealed differential expression of genes related to xenobiotic metabolism oxidative stress and carbohydrate metabolism in response to PCB exposure. In the brain PCB exposure altered the expression of genes involved in myelination and glutamate signaling. Our results suggest that there is very little correlation between DNA methylation and gene expression patterns among the differentially expressed genes DEGs. We are currently investigating the relationship between DMRs and DEGs. Overall design: Two different tissues Liver and brain from PCB126 and DMSO exposed zebrafish were analyzed for DNA methylation and gene expression using RRBS and RNAseq respectively. Four biological replicates per treatment were analyzed n=4 individual fish.,,pubmed:29686887,,CONTROL BRAIN4 RNA Seq,GSM2792794,,tissue:brain|treatment:DMSO|life history stage:Adult,CONTROL BRAIN4 RNA Seq,Enhanced RRBS data was processed by aligning the reads to the bisulfite converted genome using Bismark. CpG methylation calls were extracted from Bismark aligned bam files using MethylKit. Differential methylation analysis was carried out by SLIM method using methylKit RNAseq data was pre processed and aligned to the genome using STAR aligner and HTSeqcount was used to obtain mapped read counts Genome build: GRCz10 Supplementary files format and content: text files for RNAseq include mapped read counts; text files for ERRBS include CpG methylation calls.,brain,Adult zebrafish were exposed to either PCB126 or DMSO via waterborne exposure for xxx hours. post the exposure period fish were reared in clean water for 7 days before sampling the tissues.,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,,treatment:DMSO|life history stage:Adult,GSM2792794,GSM2792794: CONTROL BRAIN4 RNA Seq; Danio rerio; RNA Seq,GSM2792794,,1,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,GEO Accession:GSM2792794,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP118819,,,CB4_S12_L002_R1_001.fastq.gz,fastq,1463255535.0,28691285.0,GSM2792794 r1,0:51 1:0,A:408992269;C:323726908;G:309480781;T:421041726;N:13851,51,0,,,408992269,323726908,309480781,421041726,13851,SRX3214268,SRS2539008,SRA612796,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.89686,,0.19559,,0.69871,,0.50956,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2017-09-25,Adult,Adult,Brain,Nervous System 43763,SRR6072793,SRX3214267,SRS2539124,SRP118819,PRJNA412050,Integrative analysis of transcriptional and DNA methylation changes associated with PCB126 exposure in adult zebrafish Danio rerio,GSE104221,Other,The aryl hydrocarbon receptor AHR is a ligand activated transcription factor well known for mediating the toxicity of environmental chemicals such as polychlorinated biphenyls PCBs and polyaromatic hydrocarbons PAHs. There is extensive knowledge on the range of target genes regulated by AHR ligands. However there is limited information on the effect of AHR ligands on DNA methylation. The objective of this study is to investigate genome wide changes in DNA methylation and gene expression patterns in response to PCB126 exposure. Adult zebrafish were exposed to 10 nM PCB126 for 24 hours waterborne exposure and were reared in clean water for xxx days before tissue sampling. DNA methylation and transcriptional changes in the liver and brain tissues were quantified by Reduced Representation Bisulfite Sequencing RRBS and RNAseq respectively. RRBS analysis revealed DNA hypomethylation in response to PCB exposure in both liver and brain tissues. We observed 482 and 476 differentially methylated regions DMRs in the liver and brain tissues respectively. Most of the DMRs are located more than 20 kilobases upstream of the transcriptional start sites. RNAseq results from the liver revealed differential expression of genes related to xenobiotic metabolism oxidative stress and carbohydrate metabolism in response to PCB exposure. In the brain PCB exposure altered the expression of genes involved in myelination and glutamate signaling. Our results suggest that there is very little correlation between DNA methylation and gene expression patterns among the differentially expressed genes DEGs. We are currently investigating the relationship between DMRs and DEGs. Overall design: Two different tissues Liver and brain from PCB126 and DMSO exposed zebrafish were analyzed for DNA methylation and gene expression using RRBS and RNAseq respectively. Four biological replicates per treatment were analyzed n=4 individual fish.,,pubmed:29686887,,CONTROL BRAIN3 RNA Seq,GSM2792793,,tissue:brain|treatment:DMSO|life history stage:Adult,CONTROL BRAIN3 RNA Seq,Enhanced RRBS data was processed by aligning the reads to the bisulfite converted genome using Bismark. CpG methylation calls were extracted from Bismark aligned bam files using MethylKit. Differential methylation analysis was carried out by SLIM method using methylKit RNAseq data was pre processed and aligned to the genome using STAR aligner and HTSeqcount was used to obtain mapped read counts Genome build: GRCz10 Supplementary files format and content: text files for RNAseq include mapped read counts; text files for ERRBS include CpG methylation calls.,brain,Adult zebrafish were exposed to either PCB126 or DMSO via waterborne exposure for xxx hours. post the exposure period fish were reared in clean water for 7 days before sampling the tissues.,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,,treatment:DMSO|life history stage:Adult,GSM2792793,GSM2792793: CONTROL BRAIN3 RNA Seq; Danio rerio; RNA Seq,GSM2792793,,1,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,GEO Accession:GSM2792793,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP118819,,,CB3_S11_L002_R1_001.fastq.gz,fastq,1624268910.0,31848410.0,GSM2792793 r1,0:51 1:0,A:452040960;C:360441413;G:344970351;T:466800984;N:15202,51,0,,,452040960,360441413,344970351,466800984,15202,SRX3214267,SRS2539124,SRA612796,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.89974,,0.19642,,0.6896,,0.49428,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2017-09-25,Adult,Adult,Brain,Nervous System 43764,SRR6072792,SRX3214266,SRS2539123,SRP118819,PRJNA412050,Integrative analysis of transcriptional and DNA methylation changes associated with PCB126 exposure in adult zebrafish Danio rerio,GSE104221,Other,The aryl hydrocarbon receptor AHR is a ligand activated transcription factor well known for mediating the toxicity of environmental chemicals such as polychlorinated biphenyls PCBs and polyaromatic hydrocarbons PAHs. There is extensive knowledge on the range of target genes regulated by AHR ligands. However there is limited information on the effect of AHR ligands on DNA methylation. The objective of this study is to investigate genome wide changes in DNA methylation and gene expression patterns in response to PCB126 exposure. Adult zebrafish were exposed to 10 nM PCB126 for 24 hours waterborne exposure and were reared in clean water for xxx days before tissue sampling. DNA methylation and transcriptional changes in the liver and brain tissues were quantified by Reduced Representation Bisulfite Sequencing RRBS and RNAseq respectively. RRBS analysis revealed DNA hypomethylation in response to PCB exposure in both liver and brain tissues. We observed 482 and 476 differentially methylated regions DMRs in the liver and brain tissues respectively. Most of the DMRs are located more than 20 kilobases upstream of the transcriptional start sites. RNAseq results from the liver revealed differential expression of genes related to xenobiotic metabolism oxidative stress and carbohydrate metabolism in response to PCB exposure. In the brain PCB exposure altered the expression of genes involved in myelination and glutamate signaling. Our results suggest that there is very little correlation between DNA methylation and gene expression patterns among the differentially expressed genes DEGs. We are currently investigating the relationship between DMRs and DEGs. Overall design: Two different tissues Liver and brain from PCB126 and DMSO exposed zebrafish were analyzed for DNA methylation and gene expression using RRBS and RNAseq respectively. Four biological replicates per treatment were analyzed n=4 individual fish.,,pubmed:29686887,,CONTROL BRAIN2 RNA Seq,GSM2792792,,tissue:brain|treatment:DMSO|life history stage:Adult,CONTROL BRAIN2 RNA Seq,Enhanced RRBS data was processed by aligning the reads to the bisulfite converted genome using Bismark. CpG methylation calls were extracted from Bismark aligned bam files using MethylKit. Differential methylation analysis was carried out by SLIM method using methylKit RNAseq data was pre processed and aligned to the genome using STAR aligner and HTSeqcount was used to obtain mapped read counts Genome build: GRCz10 Supplementary files format and content: text files for RNAseq include mapped read counts; text files for ERRBS include CpG methylation calls.,brain,Adult zebrafish were exposed to either PCB126 or DMSO via waterborne exposure for xxx hours. post the exposure period fish were reared in clean water for 7 days before sampling the tissues.,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,,treatment:DMSO|life history stage:Adult,GSM2792792,GSM2792792: CONTROL BRAIN2 RNA Seq; Danio rerio; RNA Seq,GSM2792792,,1,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,GEO Accession:GSM2792792,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP118819,,,CB2_S10_L002_R1_001.fastq.gz,fastq,1740210678.0,34121778.0,GSM2792792 r1,0:51 1:0,A:480819797;C:388942062;G:374434527;T:495998198;N:16094,51,0,,,480819797,388942062,374434527,495998198,16094,SRX3214266,SRS2539123,SRA612796,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.91021,,0.19053,,0.68603,,0.4987,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2017-09-25,Adult,Adult,Brain,Nervous System 43765,SRR6072791,SRX3214265,SRS2539120,SRP118819,PRJNA412050,Integrative analysis of transcriptional and DNA methylation changes associated with PCB126 exposure in adult zebrafish Danio rerio,GSE104221,Other,The aryl hydrocarbon receptor AHR is a ligand activated transcription factor well known for mediating the toxicity of environmental chemicals such as polychlorinated biphenyls PCBs and polyaromatic hydrocarbons PAHs. There is extensive knowledge on the range of target genes regulated by AHR ligands. However there is limited information on the effect of AHR ligands on DNA methylation. The objective of this study is to investigate genome wide changes in DNA methylation and gene expression patterns in response to PCB126 exposure. Adult zebrafish were exposed to 10 nM PCB126 for 24 hours waterborne exposure and were reared in clean water for xxx days before tissue sampling. DNA methylation and transcriptional changes in the liver and brain tissues were quantified by Reduced Representation Bisulfite Sequencing RRBS and RNAseq respectively. RRBS analysis revealed DNA hypomethylation in response to PCB exposure in both liver and brain tissues. We observed 482 and 476 differentially methylated regions DMRs in the liver and brain tissues respectively. Most of the DMRs are located more than 20 kilobases upstream of the transcriptional start sites. RNAseq results from the liver revealed differential expression of genes related to xenobiotic metabolism oxidative stress and carbohydrate metabolism in response to PCB exposure. In the brain PCB exposure altered the expression of genes involved in myelination and glutamate signaling. Our results suggest that there is very little correlation between DNA methylation and gene expression patterns among the differentially expressed genes DEGs. We are currently investigating the relationship between DMRs and DEGs. Overall design: Two different tissues Liver and brain from PCB126 and DMSO exposed zebrafish were analyzed for DNA methylation and gene expression using RRBS and RNAseq respectively. Four biological replicates per treatment were analyzed n=4 individual fish.,,pubmed:29686887,,CONTROL BRAIN1 RNA Seq,GSM2792791,,tissue:brain|treatment:DMSO|life history stage:Adult,CONTROL BRAIN1 RNA Seq,Enhanced RRBS data was processed by aligning the reads to the bisulfite converted genome using Bismark. CpG methylation calls were extracted from Bismark aligned bam files using MethylKit. Differential methylation analysis was carried out by SLIM method using methylKit RNAseq data was pre processed and aligned to the genome using STAR aligner and HTSeqcount was used to obtain mapped read counts Genome build: GRCz10 Supplementary files format and content: text files for RNAseq include mapped read counts; text files for ERRBS include CpG methylation calls.,brain,Adult zebrafish were exposed to either PCB126 or DMSO via waterborne exposure for xxx hours. post the exposure period fish were reared in clean water for 7 days before sampling the tissues.,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,,treatment:DMSO|life history stage:Adult,GSM2792791,GSM2792791: CONTROL BRAIN1 RNA Seq; Danio rerio; RNA Seq,GSM2792791,,1,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,GEO Accession:GSM2792791,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP118819,,,CB1_S9_L002_R1_001.fastq.gz,fastq,1715146677.0,33630327.0,GSM2792791 r1,0:51 1:0,A:476861764;C:381757171;G:366051176;T:490460394;N:16172,51,0,,,476861764,381757171,366051176,490460394,16172,SRX3214265,SRS2539120,SRA612796,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.90508,,0.18823,,0.69607,,0.51563,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2017-09-25,Adult,Adult,Brain,Nervous System 53249,SRR9825129,SRX6581798,SRS5147496,SRP216250,PRJNA556200,Cross species analysis across 450 million yrs of evolution reveals conservation and divergence of the microglia program scRNA seq,GSE134705,Other,Here we characterize microglia transcriptional program across ten species spanning more than 450 million yrs of evolution. We find that microglia express a conserved core gene program of orthologous genes from rodents to human including ligands and receptors associated with interactions between glia and neurons. In most species microglia show a single dominant transcriptional state while humans express significant microglia heterogeneity. In addition we observed notable differences in complement phagocytic and several critical signaling pathways that are enriched with susceptibility genes to brain disorders including Alzheimer's and Parkinson's disease in microglia of common animal models as compared to human. Our study provides an essential resource of conserved and divergent microglia pathways across evolution with important implications for future development of microglia based therapies in humans. Overall design: Single cell and bulk RNA seq of microglia from 10 different species and comparison of transcriptional landcape over species. Biological replicates of different species were n=3 6.,parent bioproject:PRJNA556197,pubmed:31835035,,AB7155,GSM3963895,,source name:Total brain|strain:WT|tissue:Brain|cell type:Immune cells|selection marker:Ib4|source:Thermo Fisher|age:4 5mo,AB7155,"bcl2fastq/2.15.0.4 Sequences with RMT of low quality defined as RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT while ""NNNNNN"" was used as a place holders if plate barcode was not used. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Genome build: hg38 Genome build: Mmul 8.0.1 Genome build: calJac3 Genome build: Oar v3.1 Genome build: Rnor 6.0 Genome build: mm10 Genome build: S.galili v1.0 Genome build: MesAur1.0 Genome build: galGal5 Genome build: danRer10 Supplementary files format and content: tab delimited text files include mRNA molecule count values for each Sample",Total brain,,Single cell libraries were prepared as previously described Keren Shaul Nature Protocols 2019. In brief mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription and the resulting RNA is fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier Keren Shaul Nature Protocols 2019. Single cell RNA seq libraries were prepared as previously described {Jaitin 2014}. In brief mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription and the resulting RNA was fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin 2014},,strain:WT|tissue:Brain|cell type:Immune cells|selection marker:Ib4|source:Thermo Fisher|catalog#:I32450|age:4 5mo,GSM3963895,GSM3963895: AB7155; Danio rerio; RNA Seq,GSM3963895,,1,Single cell libraries were prepared as previously described Keren Shaul Nature Protocols 2019. In brief mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription and the resulting RNA is fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier Keren Shaul Nature Protocols 2019. Single cell RNA seq libraries were prepared as previously described {Jaitin 2014}. In brief mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription and the resulting RNA was fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin 2014},GEO Accession:GSM3963895,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP216250,,loader:fastq load.py|options: appendBCtoName,AB7155_SB343_S29_R1_001.fastq.gz,fastq,1139724267.0,16517743.0,GSM3963895 r1,0:69,A:331549647;C:254056286;G:280458785;T:273550294;N:109255,69,,,,331549647,254056286,280458785,273550294,109255,SRX6581798,SRS5147496,SRA926018,GEO,"Immunology, Weizmann Institute of Science",1,0.90535,,0.17532,,0.87803,,0.67683,,69,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc_generic,bulk,bulk,,Israel,2019-07-23,Undetermined,Undetermined,Brain,Nervous System 53250,SRR9825128,SRX6581797,SRS5147495,SRP216250,PRJNA556200,Cross species analysis across 450 million yrs of evolution reveals conservation and divergence of the microglia program scRNA seq,GSE134705,Other,Here we characterize microglia transcriptional program across ten species spanning more than 450 million yrs of evolution. We find that microglia express a conserved core gene program of orthologous genes from rodents to human including ligands and receptors associated with interactions between glia and neurons. In most species microglia show a single dominant transcriptional state while humans express significant microglia heterogeneity. In addition we observed notable differences in complement phagocytic and several critical signaling pathways that are enriched with susceptibility genes to brain disorders including Alzheimer's and Parkinson's disease in microglia of common animal models as compared to human. Our study provides an essential resource of conserved and divergent microglia pathways across evolution with important implications for future development of microglia based therapies in humans. Overall design: Single cell and bulk RNA seq of microglia from 10 different species and comparison of transcriptional landcape over species. Biological replicates of different species were n=3 6.,parent bioproject:PRJNA556197,pubmed:31835035,,AB7154,GSM3963894,,source name:Total brain|strain:WT|tissue:Brain|cell type:Immune cells|selection marker:Ib4|source:Thermo Fisher|age:4 5mo,AB7154,"bcl2fastq/2.15.0.4 Sequences with RMT of low quality defined as RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT while ""NNNNNN"" was used as a place holders if plate barcode was not used. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Genome build: hg38 Genome build: Mmul 8.0.1 Genome build: calJac3 Genome build: Oar v3.1 Genome build: Rnor 6.0 Genome build: mm10 Genome build: S.galili v1.0 Genome build: MesAur1.0 Genome build: galGal5 Genome build: danRer10 Supplementary files format and content: tab delimited text files include mRNA molecule count values for each Sample",Total brain,,Single cell libraries were prepared as previously described Keren Shaul Nature Protocols 2019. In brief mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription and the resulting RNA is fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier Keren Shaul Nature Protocols 2019. Single cell RNA seq libraries were prepared as previously described {Jaitin 2014}. In brief mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription and the resulting RNA was fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin 2014},,strain:WT|tissue:Brain|cell type:Immune cells|selection marker:Ib4|source:Thermo Fisher|catalog#:I32450|age:4 5mo,GSM3963894,GSM3963894: AB7154; Danio rerio; RNA Seq,GSM3963894,,1,Single cell libraries were prepared as previously described Keren Shaul Nature Protocols 2019. In brief mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription and the resulting RNA is fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier Keren Shaul Nature Protocols 2019. Single cell RNA seq libraries were prepared as previously described {Jaitin 2014}. In brief mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription and the resulting RNA was fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin 2014},GEO Accession:GSM3963894,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP216250,,loader:fastq load.py|options: appendBCtoName,AB7154_SB343_S36_R1_001.fastq.gz,fastq,1161384609.0,16831661.0,GSM3963894 r1,0:69,A:337010566;C:261723350;G:290674768;T:271864761;N:111164,69,,,,337010566,261723350,290674768,271864761,111164,SRX6581797,SRS5147495,SRA926018,GEO,"Immunology, Weizmann Institute of Science",1,0.89031,,0.18199,,0.88154,,0.67975,,69,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc_generic,bulk,bulk,,Israel,2019-07-23,Undetermined,Undetermined,Brain,Nervous System 53251,SRR9825127,SRX6581796,SRS5147494,SRP216250,PRJNA556200,Cross species analysis across 450 million yrs of evolution reveals conservation and divergence of the microglia program scRNA seq,GSE134705,Other,Here we characterize microglia transcriptional program across ten species spanning more than 450 million yrs of evolution. We find that microglia express a conserved core gene program of orthologous genes from rodents to human including ligands and receptors associated with interactions between glia and neurons. In most species microglia show a single dominant transcriptional state while humans express significant microglia heterogeneity. In addition we observed notable differences in complement phagocytic and several critical signaling pathways that are enriched with susceptibility genes to brain disorders including Alzheimer's and Parkinson's disease in microglia of common animal models as compared to human. Our study provides an essential resource of conserved and divergent microglia pathways across evolution with important implications for future development of microglia based therapies in humans. Overall design: Single cell and bulk RNA seq of microglia from 10 different species and comparison of transcriptional landcape over species. Biological replicates of different species were n=3 6.,parent bioproject:PRJNA556197,pubmed:31835035,,AB7153,GSM3963893,,source name:Total brain|strain:WT|tissue:Brain|cell type:Immune cells|selection marker:Ib4|source:Thermo Fisher|age:4 5mo,AB7153,"bcl2fastq/2.15.0.4 Sequences with RMT of low quality defined as RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT while ""NNNNNN"" was used as a place holders if plate barcode was not used. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Genome build: hg38 Genome build: Mmul 8.0.1 Genome build: calJac3 Genome build: Oar v3.1 Genome build: Rnor 6.0 Genome build: mm10 Genome build: S.galili v1.0 Genome build: MesAur1.0 Genome build: galGal5 Genome build: danRer10 Supplementary files format and content: tab delimited text files include mRNA molecule count values for each Sample",Total brain,,Single cell libraries were prepared as previously described Keren Shaul Nature Protocols 2019. In brief mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription and the resulting RNA is fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier Keren Shaul Nature Protocols 2019. Single cell RNA seq libraries were prepared as previously described {Jaitin 2014}. In brief mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription and the resulting RNA was fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin 2014},,strain:WT|tissue:Brain|cell type:Immune cells|selection marker:Ib4|source:Thermo Fisher|catalog#:I32450|age:4 5mo,GSM3963893,GSM3963893: AB7153; Danio rerio; RNA Seq,GSM3963893,,1,Single cell libraries were prepared as previously described Keren Shaul Nature Protocols 2019. In brief mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription and the resulting RNA is fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier Keren Shaul Nature Protocols 2019. Single cell RNA seq libraries were prepared as previously described {Jaitin 2014}. In brief mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription and the resulting RNA was fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin 2014},GEO Accession:GSM3963893,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP216250,,loader:fastq load.py|options: appendBCtoName,AB7153_SB343_S44_R1_001.fastq.gz,fastq,1088811030.0,15779870.0,GSM3963893 r1,0:69,A:320167297;C:243538818;G:266263775;T:258739754;N:101386,69,,,,320167297,243538818,266263775,258739754,101386,SRX6581796,SRS5147494,SRA926018,GEO,"Immunology, Weizmann Institute of Science",1,0.89179,,0.12861,,0.87259,,0.63828,,69,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc_generic,bulk,bulk,,Israel,2019-07-23,Undetermined,Undetermined,Brain,Nervous System 53252,SRR9825125,SRX6581795,SRS5147493,SRP216250,PRJNA556200,Cross species analysis across 450 million yrs of evolution reveals conservation and divergence of the microglia program scRNA seq,GSE134705,Other,Here we characterize microglia transcriptional program across ten species spanning more than 450 million yrs of evolution. We find that microglia express a conserved core gene program of orthologous genes from rodents to human including ligands and receptors associated with interactions between glia and neurons. In most species microglia show a single dominant transcriptional state while humans express significant microglia heterogeneity. In addition we observed notable differences in complement phagocytic and several critical signaling pathways that are enriched with susceptibility genes to brain disorders including Alzheimer's and Parkinson's disease in microglia of common animal models as compared to human. Our study provides an essential resource of conserved and divergent microglia pathways across evolution with important implications for future development of microglia based therapies in humans. Overall design: Single cell and bulk RNA seq of microglia from 10 different species and comparison of transcriptional landcape over species. Biological replicates of different species were n=3 6.,parent bioproject:PRJNA556197,pubmed:31835035,,AB5657,GSM3963892,,source name:Total brain|strain:eGFP mPEG|tissue:Brain|cell type:Immune cells|selection marker:mPEG GFP|source:NA|age:4 5mo,AB5657,"bcl2fastq/2.15.0.4 Sequences with RMT of low quality defined as RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT while ""NNNNNN"" was used as a place holders if plate barcode was not used. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Genome build: hg38 Genome build: Mmul 8.0.1 Genome build: calJac3 Genome build: Oar v3.1 Genome build: Rnor 6.0 Genome build: mm10 Genome build: S.galili v1.0 Genome build: MesAur1.0 Genome build: galGal5 Genome build: danRer10 Supplementary files format and content: tab delimited text files include mRNA molecule count values for each Sample",Total brain,,Single cell libraries were prepared as previously described Keren Shaul Nature Protocols 2019. In brief mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription and the resulting RNA is fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier Keren Shaul Nature Protocols 2019. Single cell RNA seq libraries were prepared as previously described {Jaitin 2014}. In brief mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription and the resulting RNA was fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin 2014},,strain:eGFP mPEG|tissue:Brain|cell type:Immune cells|selection marker:mPEG GFP|source:NA|catalog#:NA|age:4 5mo,GSM3963892,GSM3963892: AB5657; Danio rerio; RNA Seq,GSM3963892,,1,Single cell libraries were prepared as previously described Keren Shaul Nature Protocols 2019. In brief mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription and the resulting RNA is fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier Keren Shaul Nature Protocols 2019. Single cell RNA seq libraries were prepared as previously described {Jaitin 2014}. In brief mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription and the resulting RNA was fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin 2014},GEO Accession:GSM3963892,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP216250,,loader:fastq load.py|options: appendBCtoName,AB5657_SB283_S14_R1_001.fastq.gz,fastq,331332549.0,4801921.0,GSM3963892 r1,0:69,A:89857088;C:69771659;G:81302142;T:90395650;N:6010,69,,,,89857088,69771659,81302142,90395650,6010,SRX6581795,SRS5147493,SRA926018,GEO,"Immunology, Weizmann Institute of Science",1,0.88981,,0.33973,,0.93507,,0.6341,,69,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc_generic,bulk,bulk,,Israel,2019-07-23,Undetermined,Undetermined,Brain,Nervous System 53253,SRR9825126,SRX6581795,SRS5147493,SRP216250,PRJNA556200,Cross species analysis across 450 million yrs of evolution reveals conservation and divergence of the microglia program scRNA seq,GSE134705,Other,Here we characterize microglia transcriptional program across ten species spanning more than 450 million yrs of evolution. We find that microglia express a conserved core gene program of orthologous genes from rodents to human including ligands and receptors associated with interactions between glia and neurons. In most species microglia show a single dominant transcriptional state while humans express significant microglia heterogeneity. In addition we observed notable differences in complement phagocytic and several critical signaling pathways that are enriched with susceptibility genes to brain disorders including Alzheimer's and Parkinson's disease in microglia of common animal models as compared to human. Our study provides an essential resource of conserved and divergent microglia pathways across evolution with important implications for future development of microglia based therapies in humans. Overall design: Single cell and bulk RNA seq of microglia from 10 different species and comparison of transcriptional landcape over species. Biological replicates of different species were n=3 6.,parent bioproject:PRJNA556197,pubmed:31835035,,AB5657,GSM3963892,,source name:Total brain|strain:eGFP mPEG|tissue:Brain|cell type:Immune cells|selection marker:mPEG GFP|source:NA|age:4 5mo,AB5657,"bcl2fastq/2.15.0.4 Sequences with RMT of low quality defined as RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT while ""NNNNNN"" was used as a place holders if plate barcode was not used. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Genome build: hg38 Genome build: Mmul 8.0.1 Genome build: calJac3 Genome build: Oar v3.1 Genome build: Rnor 6.0 Genome build: mm10 Genome build: S.galili v1.0 Genome build: MesAur1.0 Genome build: galGal5 Genome build: danRer10 Supplementary files format and content: tab delimited text files include mRNA molecule count values for each Sample",Total brain,,Single cell libraries were prepared as previously described Keren Shaul Nature Protocols 2019. In brief mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription and the resulting RNA is fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier Keren Shaul Nature Protocols 2019. Single cell RNA seq libraries were prepared as previously described {Jaitin 2014}. In brief mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription and the resulting RNA was fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin 2014},,strain:eGFP mPEG|tissue:Brain|cell type:Immune cells|selection marker:mPEG GFP|source:NA|catalog#:NA|age:4 5mo,GSM3963892,GSM3963892: AB5657; Danio rerio; RNA Seq,GSM3963892,,1,Single cell libraries were prepared as previously described Keren Shaul Nature Protocols 2019. In brief mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription and the resulting RNA is fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier Keren Shaul Nature Protocols 2019. Single cell RNA seq libraries were prepared as previously described {Jaitin 2014}. In brief mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription and the resulting RNA was fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin 2014},GEO Accession:GSM3963892,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP216250,,loader:fastq load.py|options: appendBCtoName,AB5657_SB284_S3_R1_001.fastq.gz,fastq,796908117.0,11549393.0,GSM3963892 r2,0:69,A:223319161;C:173475726;G:194239433;T:205842249;N:31548,69,,,,223319161,173475726,194239433,205842249,31548,SRX6581795,SRS5147493,SRA926018,GEO,"Immunology, Weizmann Institute of Science",1,0.8909,,0.30223,,0.91802,,0.65318,,69,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc_generic,bulk,bulk,,Israel,2019-07-23,Undetermined,Undetermined,Brain,Nervous System 53254,SRR9825124,SRX6581794,SRS5147492,SRP216250,PRJNA556200,Cross species analysis across 450 million yrs of evolution reveals conservation and divergence of the microglia program scRNA seq,GSE134705,Other,Here we characterize microglia transcriptional program across ten species spanning more than 450 million yrs of evolution. We find that microglia express a conserved core gene program of orthologous genes from rodents to human including ligands and receptors associated with interactions between glia and neurons. In most species microglia show a single dominant transcriptional state while humans express significant microglia heterogeneity. In addition we observed notable differences in complement phagocytic and several critical signaling pathways that are enriched with susceptibility genes to brain disorders including Alzheimer's and Parkinson's disease in microglia of common animal models as compared to human. Our study provides an essential resource of conserved and divergent microglia pathways across evolution with important implications for future development of microglia based therapies in humans. Overall design: Single cell and bulk RNA seq of microglia from 10 different species and comparison of transcriptional landcape over species. Biological replicates of different species were n=3 6.,parent bioproject:PRJNA556197,pubmed:31835035,,AB3014,GSM3963891,,source name:Total brain|strain:eGFP mPEG|tissue:Brain|cell type:Immune cells|selection marker:mPEG GFP|source:NA|age:4 5mo,AB3014,"bcl2fastq/2.15.0.4 Sequences with RMT of low quality defined as RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT while ""NNNNNN"" was used as a place holders if plate barcode was not used. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Genome build: hg38 Genome build: Mmul 8.0.1 Genome build: calJac3 Genome build: Oar v3.1 Genome build: Rnor 6.0 Genome build: mm10 Genome build: S.galili v1.0 Genome build: MesAur1.0 Genome build: galGal5 Genome build: danRer10 Supplementary files format and content: tab delimited text files include mRNA molecule count values for each Sample",Total brain,,Single cell libraries were prepared as previously described Keren Shaul Nature Protocols 2019. In brief mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription and the resulting RNA is fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier Keren Shaul Nature Protocols 2019. Single cell RNA seq libraries were prepared as previously described {Jaitin 2014}. In brief mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription and the resulting RNA was fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin 2014},,strain:eGFP mPEG|tissue:Brain|cell type:Immune cells|selection marker:mPEG GFP|source:NA|catalog#:NA|age:4 5mo,GSM3963891,GSM3963891: AB3014; Danio rerio; RNA Seq,GSM3963891,,1,Single cell libraries were prepared as previously described Keren Shaul Nature Protocols 2019. In brief mRNA from cell sorted into cell capture plates are barcoded and converted into cDNA and pooled using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription and the resulting RNA is fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration is assessed as described earlier Keren Shaul Nature Protocols 2019. Single cell RNA seq libraries were prepared as previously described {Jaitin 2014}. In brief mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription and the resulting RNA was fragmented and converted into a sequencing ready library by tagging the samples with pool barcodes and Illumina sequences during ligation RT and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin 2014},GEO Accession:GSM3963891,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP216250,,loader:fastq load.py|options: appendBCtoName,AB3014.fastq.gz,fastq,1854197730.0,28093905.0,GSM3963891 r1,0:66,A:546306466;C:392206824;G:436944803;T:478712291;N:27346,66,,,,546306466,392206824,436944803,478712291,27346,SRX6581794,SRS5147492,SRA926018,GEO,"Immunology, Weizmann Institute of Science",1,0.90278,,0.4347,,0.88925,,0.64871,,66,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc_generic,bulk,bulk,,Israel,2019-07-23,Undetermined,Undetermined,Brain,Nervous System 61837,SRR12999696,SRX9450941,SRS7663855,SRP291443,PRJNA675087,MicroRNAs involved in regeneration of adult zebrafish brain.,GSE160992,Transcriptome Analysis,For its remarkable ability to heal injuries of the adult central nervous system the zebrafish has become an important model to investigate neural regeneration. Despite big progresses in our understanding of some of the underlying key processes a comprehensive analysis of the changes of the transcriptome has not been reported yet. We analysed here the transcriptome of the regenerating telencephalon for changes in the expression of microRNAs and their putative targets. Overall design: small RNA sequencing of injured and control adult zebrafish telencephalic hemisphere,,pubmed:34054419;pubmed:35204047,,injured telencephalic hemisphere 3,GSM4887529,,source name:telencephalic hemisphere|tissue:telencephalon|treatment:injury,injured telencephalic hemisphere 3,Run was demultiplexed with bcl2fasq Adaptor sequence was trimmed from reads with cutadapt Reads were mapped with bwa Raw level of expression was computed with HTSeq Genome build: GRCz11 Supplementary files format and content: raw count per gene,telencephalic hemisphere,,Trizol Invitrogen From 1µg of total RNAs we prepared libraries with the TruSeq Total RNA library preparation kit from Illumina and following Illumina's recommendations. We then selected molecule of libraries according to their size with a migration on a polyacrylamide gel. Quality of input RNAs and libraries were both assessed with a BioAnalyzer 2100. The libraries were prepared in triplicates for both conditions control and injured.,,tissue:telencephalon|treatment:injury,GSM4887529,GSM4887529: injured telencephalic hemisphere 3; Danio rerio; RNA Seq,GSM4887529,,1,Trizol Invitrogen TrueSeq RNA Illumina,GEO Accession:GSM4887529,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP291443,,,STAB3.fastq.gz,fastq,1424796409.0,65132630.0,GSM4887529 r1,0:21.88 1:0,A:333355914;C:282050013;G:361225960;T:448164522;N:0,21,0,,,333355914,282050013,361225960,448164522,0,SRX9450941,SRS7663855,SRA1155190,GEO,"UMR1064, Centre de recherche en transplantation et immunologie",1,0.92334,,0.08864,,0.97611,,0.54523,,22,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,bulk,bulk,,Canada,2020-11-06,Undetermined,Adult,Brain,Nervous System 61838,SRR12999695,SRX9450940,SRS7663854,SRP291443,PRJNA675087,MicroRNAs involved in regeneration of adult zebrafish brain.,GSE160992,Transcriptome Analysis,For its remarkable ability to heal injuries of the adult central nervous system the zebrafish has become an important model to investigate neural regeneration. Despite big progresses in our understanding of some of the underlying key processes a comprehensive analysis of the changes of the transcriptome has not been reported yet. We analysed here the transcriptome of the regenerating telencephalon for changes in the expression of microRNAs and their putative targets. Overall design: small RNA sequencing of injured and control adult zebrafish telencephalic hemisphere,,pubmed:34054419;pubmed:35204047,,injured telencephalic hemisphere 2,GSM4887528,,source name:telencephalic hemisphere|tissue:telencephalon|treatment:injury,injured telencephalic hemisphere 2,Run was demultiplexed with bcl2fasq Adaptor sequence was trimmed from reads with cutadapt Reads were mapped with bwa Raw level of expression was computed with HTSeq Genome build: GRCz11 Supplementary files format and content: raw count per gene,telencephalic hemisphere,,Trizol Invitrogen From 1µg of total RNAs we prepared libraries with the TruSeq Total RNA library preparation kit from Illumina and following Illumina's recommendations. We then selected molecule of libraries according to their size with a migration on a polyacrylamide gel. Quality of input RNAs and libraries were both assessed with a BioAnalyzer 2100. The libraries were prepared in triplicates for both conditions control and injured.,,tissue:telencephalon|treatment:injury,GSM4887528,GSM4887528: injured telencephalic hemisphere 2; Danio rerio; RNA Seq,GSM4887528,,1,Trizol Invitrogen TrueSeq RNA Illumina,GEO Accession:GSM4887528,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP291443,,,STAB2.fastq.gz,fastq,1492088541.0,67892332.0,GSM4887528 r1,0:21.98 1:0,A:349593244;C:293016325;G:377668555;T:471810417;N:0,21,0,,,349593244,293016325,377668555,471810417,0,SRX9450940,SRS7663854,SRA1155190,GEO,"UMR1064, Centre de recherche en transplantation et immunologie",1,0.93253,,0.08588,,0.97666,,0.54494,,22,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,bulk,bulk,,Canada,2020-11-06,Undetermined,Adult,Brain,Nervous System 61839,SRR12999694,SRX9450939,SRS7663853,SRP291443,PRJNA675087,MicroRNAs involved in regeneration of adult zebrafish brain.,GSE160992,Transcriptome Analysis,For its remarkable ability to heal injuries of the adult central nervous system the zebrafish has become an important model to investigate neural regeneration. Despite big progresses in our understanding of some of the underlying key processes a comprehensive analysis of the changes of the transcriptome has not been reported yet. We analysed here the transcriptome of the regenerating telencephalon for changes in the expression of microRNAs and their putative targets. Overall design: small RNA sequencing of injured and control adult zebrafish telencephalic hemisphere,,pubmed:34054419;pubmed:35204047,,injured telencephalic hemisphere 1,GSM4887527,,source name:telencephalic hemisphere|tissue:telencephalon|treatment:injury,injured telencephalic hemisphere 1,Run was demultiplexed with bcl2fasq Adaptor sequence was trimmed from reads with cutadapt Reads were mapped with bwa Raw level of expression was computed with HTSeq Genome build: GRCz11 Supplementary files format and content: raw count per gene,telencephalic hemisphere,,Trizol Invitrogen From 1µg of total RNAs we prepared libraries with the TruSeq Total RNA library preparation kit from Illumina and following Illumina's recommendations. We then selected molecule of libraries according to their size with a migration on a polyacrylamide gel. Quality of input RNAs and libraries were both assessed with a BioAnalyzer 2100. The libraries were prepared in triplicates for both conditions control and injured.,,tissue:telencephalon|treatment:injury,GSM4887527,GSM4887527: injured telencephalic hemisphere 1; Danio rerio; RNA Seq,GSM4887527,,1,Trizol Invitrogen TrueSeq RNA Illumina,GEO Accession:GSM4887527,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP291443,,,STAB1.fastq.gz,fastq,1915689209.0,87803695.0,GSM4887527 r1,0:21.82 1:0,A:446653242;C:378509659;G:482923940;T:607602368;N:0,21,0,,,446653242,378509659,482923940,607602368,0,SRX9450939,SRS7663853,SRA1155190,GEO,"UMR1064, Centre de recherche en transplantation et immunologie",1,0.91949,,0.08917,,0.97954,,0.53009,,21,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,bulk,bulk,,Canada,2020-11-06,Undetermined,Adult,Brain,Nervous System 61840,SRR12999693,SRX9450938,SRS7663852,SRP291443,PRJNA675087,MicroRNAs involved in regeneration of adult zebrafish brain.,GSE160992,Transcriptome Analysis,For its remarkable ability to heal injuries of the adult central nervous system the zebrafish has become an important model to investigate neural regeneration. Despite big progresses in our understanding of some of the underlying key processes a comprehensive analysis of the changes of the transcriptome has not been reported yet. We analysed here the transcriptome of the regenerating telencephalon for changes in the expression of microRNAs and their putative targets. Overall design: small RNA sequencing of injured and control adult zebrafish telencephalic hemisphere,,pubmed:34054419;pubmed:35204047,,healthy telencephalic hemisphere 3,GSM4887526,,source name:telencephalic hemisphere|tissue:telencephalon|treatment:no treatment,healthy telencephalic hemisphere 3,Run was demultiplexed with bcl2fasq Adaptor sequence was trimmed from reads with cutadapt Reads were mapped with bwa Raw level of expression was computed with HTSeq Genome build: GRCz11 Supplementary files format and content: raw count per gene,telencephalic hemisphere,,Trizol Invitrogen From 1µg of total RNAs we prepared libraries with the TruSeq Total RNA library preparation kit from Illumina and following Illumina's recommendations. We then selected molecule of libraries according to their size with a migration on a polyacrylamide gel. Quality of input RNAs and libraries were both assessed with a BioAnalyzer 2100. The libraries were prepared in triplicates for both conditions control and injured.,,tissue:telencephalon|treatment:no treatment,GSM4887526,GSM4887526: healthy telencephalic hemisphere 3; Danio rerio; RNA Seq,GSM4887526,,1,Trizol Invitrogen TrueSeq RNA Illumina,GEO Accession:GSM4887526,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP291443,,,CTRL3.fastq.gz,fastq,323568644.0,14847336.0,GSM4887526 r1,0:21.79 1:0,A:75720892;C:64438959;G:80940855;T:102467938;N:0,21,0,,,75720892,64438959,80940855,102467938,0,SRX9450938,SRS7663852,SRA1155190,GEO,"UMR1064, Centre de recherche en transplantation et immunologie",1,0.91791,,0.08755,,0.98054,,0.5616,,22,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,bulk,bulk,,Canada,2020-11-06,Undetermined,Adult,Brain,Nervous System 61841,SRR12999692,SRX9450937,SRS7663851,SRP291443,PRJNA675087,MicroRNAs involved in regeneration of adult zebrafish brain.,GSE160992,Transcriptome Analysis,For its remarkable ability to heal injuries of the adult central nervous system the zebrafish has become an important model to investigate neural regeneration. Despite big progresses in our understanding of some of the underlying key processes a comprehensive analysis of the changes of the transcriptome has not been reported yet. We analysed here the transcriptome of the regenerating telencephalon for changes in the expression of microRNAs and their putative targets. Overall design: small RNA sequencing of injured and control adult zebrafish telencephalic hemisphere,,pubmed:34054419;pubmed:35204047,,healthy telencephalic hemisphere 2,GSM4887525,,source name:telencephalic hemisphere|tissue:telencephalon|treatment:no treatment,healthy telencephalic hemisphere 2,Run was demultiplexed with bcl2fasq Adaptor sequence was trimmed from reads with cutadapt Reads were mapped with bwa Raw level of expression was computed with HTSeq Genome build: GRCz11 Supplementary files format and content: raw count per gene,telencephalic hemisphere,,Trizol Invitrogen From 1µg of total RNAs we prepared libraries with the TruSeq Total RNA library preparation kit from Illumina and following Illumina's recommendations. We then selected molecule of libraries according to their size with a migration on a polyacrylamide gel. Quality of input RNAs and libraries were both assessed with a BioAnalyzer 2100. The libraries were prepared in triplicates for both conditions control and injured.,,tissue:telencephalon|treatment:no treatment,GSM4887525,GSM4887525: healthy telencephalic hemisphere 2; Danio rerio; RNA Seq,GSM4887525,,1,Trizol Invitrogen TrueSeq RNA Illumina,GEO Accession:GSM4887525,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP291443,,,CTRL2.fastq.gz,fastq,533253402.0,24364720.0,GSM4887525 r1,0:21.89 1:0,A:125553872;C:106408524;G:133237076;T:168053930;N:0,21,0,,,125553872,106408524,133237076,168053930,0,SRX9450937,SRS7663851,SRA1155190,GEO,"UMR1064, Centre de recherche en transplantation et immunologie",1,0.92261,,0.08906,,0.97881,,0.55986,,21,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,bulk,bulk,,Canada,2020-11-06,Undetermined,Adult,Brain,Nervous System 61842,SRR12999691,SRX9450936,SRS7663850,SRP291443,PRJNA675087,MicroRNAs involved in regeneration of adult zebrafish brain.,GSE160992,Transcriptome Analysis,For its remarkable ability to heal injuries of the adult central nervous system the zebrafish has become an important model to investigate neural regeneration. Despite big progresses in our understanding of some of the underlying key processes a comprehensive analysis of the changes of the transcriptome has not been reported yet. We analysed here the transcriptome of the regenerating telencephalon for changes in the expression of microRNAs and their putative targets. Overall design: small RNA sequencing of injured and control adult zebrafish telencephalic hemisphere,,pubmed:34054419;pubmed:35204047,,healthy telencephalic hemisphere 1,GSM4887524,,source name:telencephalic hemisphere|tissue:telencephalon|treatment:no treatment,healthy telencephalic hemisphere 1,Run was demultiplexed with bcl2fasq Adaptor sequence was trimmed from reads with cutadapt Reads were mapped with bwa Raw level of expression was computed with HTSeq Genome build: GRCz11 Supplementary files format and content: raw count per gene,telencephalic hemisphere,,Trizol Invitrogen From 1µg of total RNAs we prepared libraries with the TruSeq Total RNA library preparation kit from Illumina and following Illumina's recommendations. We then selected molecule of libraries according to their size with a migration on a polyacrylamide gel. Quality of input RNAs and libraries were both assessed with a BioAnalyzer 2100. The libraries were prepared in triplicates for both conditions control and injured.,,tissue:telencephalon|treatment:no treatment,GSM4887524,GSM4887524: healthy telencephalic hemisphere 1; Danio rerio; RNA Seq,GSM4887524,,1,Trizol Invitrogen TrueSeq RNA Illumina,GEO Accession:GSM4887524,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP291443,,,CTRL1.fastq.gz,fastq,347713277.0,15928765.0,GSM4887524 r1,0:21.83 1:0,A:81497309;C:69157722;G:86472353;T:110585893;N:0,21,0,,,81497309,69157722,86472353,110585893,0,SRX9450936,SRS7663850,SRA1155190,GEO,"UMR1064, Centre de recherche en transplantation et immunologie",1,0.91979,,0.0902,,0.96512,,0.56094,,22,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,bulk,bulk,,Canada,2020-11-06,Undetermined,Adult,Brain,Nervous System 77303,SRR25453755,SRX21186685,SRS18446706,SRP452071,PRJNA999746,Transcriptomic differences between deeply quiescent and activated adult NSCs,GSE239594,Transcriptome Analysis,To identify pathways regulating NSC quiescence with a possible link to quiescence depth we used double transgenic Tgher4:drfp;Tgmcm5:gfp fish and paradigms predicted to highlight deep vs shallower quiescence. In adult fish 3 mpf mpf we performed bulk RNA sequencing on FACS sorted RFPhigh GFPneg qNSCs expressing strongly her4 signing NSCs transcriptionally remote from activation and activated NSCs. Overall design: To investigate transcriptomic differences between adult deeply quiescent NSCs and activated NSCs we performed bulk RNA Seq,parent bioproject:PRJNA999741,pubmed:38518783,,Experiment 13 tgher4:RFP low,GSM7668467,,source name:brain/telencephali|tissue:brain/telencephali|genotype:tgher4:RFP low|age:3 mpf|nsc status:Quiescent low expression of her4.3|condition:L|replicate:r13|geo loc name:missing|collection date:missing,Experiment 13 tgher4:RFP low,Reads were mapped to zebrafish genome using STAR Gene counts were computed using featureCounts Differential expression analysis was performed with DESeq2 Assembly: GRCz10 Supplementary files format and content: Tab delimited text file with gene Ids and their respective counts,brain/telencephali,,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,tissue:brain/telencephali|genotype:tgher4:RFP low|age:3 mpf|nsc status:Quiescent low expression of her4.3|condition:L|replicate:r13,GSM7668467,GSM7668467: Experiment 13 tgher4:RFP low; Danio rerio; RNA Seq,GSM7668467 r1,GSM7668467,1,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP452071,,,13RL.fastq.gz,fastq,2089168000.0,32643250.0,GSM7668467 r1,0:64,A:491435480;C:556848569;G:626704317;T:414165769;N:13865,64,,,,491435480,556848569,626704317,414165769,13865,SRX21186685,SRS18446706,SRA1683289,Institut Pasteur,Institut Pasteur,1,0.8119,,0.23552,,0.78575,,0.66137,,64,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,France,2023-07-28,Adult,Adult,Brain,Nervous System 77304,SRR25453756,SRX21186684,SRS18446705,SRP452071,PRJNA999746,Transcriptomic differences between deeply quiescent and activated adult NSCs,GSE239594,Transcriptome Analysis,To identify pathways regulating NSC quiescence with a possible link to quiescence depth we used double transgenic Tgher4:drfp;Tgmcm5:gfp fish and paradigms predicted to highlight deep vs shallower quiescence. In adult fish 3 mpf mpf we performed bulk RNA sequencing on FACS sorted RFPhigh GFPneg qNSCs expressing strongly her4 signing NSCs transcriptionally remote from activation and activated NSCs. Overall design: To investigate transcriptomic differences between adult deeply quiescent NSCs and activated NSCs we performed bulk RNA Seq,parent bioproject:PRJNA999741,pubmed:38518783,,Experiment 13 tgher4:RFP high,GSM7668466,,source name:brain/telencephali|tissue:brain/telencephali|genotype:tgher4:RFP high|age:3 mpf|nsc status:Quiescent highly expressing her4.3|condition:H|replicate:r13|geo loc name:missing|collection date:missing,Experiment 13 tgher4:RFP high,Reads were mapped to zebrafish genome using STAR Gene counts were computed using featureCounts Differential expression analysis was performed with DESeq2 Assembly: GRCz10 Supplementary files format and content: Tab delimited text file with gene Ids and their respective counts,brain/telencephali,,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,tissue:brain/telencephali|genotype:tgher4:RFP high|age:3 mpf|nsc status:Quiescent highly expressing her4.3|condition:H|replicate:r13,GSM7668466,GSM7668466: Experiment 13 tgher4:RFP high; Danio rerio; RNA Seq,GSM7668466 r1,GSM7668466,1,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP452071,,,13RH.fastq.gz,fastq,1736530176.0,27133284.0,GSM7668466 r1,0:64,A:421791163;C:450901073;G:507159612;T:356667757;N:10571,64,,,,421791163,450901073,507159612,356667757,10571,SRX21186684,SRS18446705,SRA1683289,Institut Pasteur,Institut Pasteur,1,0.86128,,0.27411,,0.76187,,0.61881,,64,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,France,2023-07-28,Adult,Adult,Brain,Nervous System 77305,SRR25453758,SRX21186682,SRS18446703,SRP452071,PRJNA999746,Transcriptomic differences between deeply quiescent and activated adult NSCs,GSE239594,Transcriptome Analysis,To identify pathways regulating NSC quiescence with a possible link to quiescence depth we used double transgenic Tgher4:drfp;Tgmcm5:gfp fish and paradigms predicted to highlight deep vs shallower quiescence. In adult fish 3 mpf mpf we performed bulk RNA sequencing on FACS sorted RFPhigh GFPneg qNSCs expressing strongly her4 signing NSCs transcriptionally remote from activation and activated NSCs. Overall design: To investigate transcriptomic differences between adult deeply quiescent NSCs and activated NSCs we performed bulk RNA Seq,parent bioproject:PRJNA999741,pubmed:38518783,,Experiment 12 tgher4:RFP low,GSM7668464,,source name:brain/telencephali|tissue:brain/telencephali|genotype:tgher4:RFP low|age:3 mpf|nsc status:Quiescent low expression of her4.3|condition:L|replicate:r12|geo loc name:missing|collection date:missing,Experiment 12 tgher4:RFP low,Reads were mapped to zebrafish genome using STAR Gene counts were computed using featureCounts Differential expression analysis was performed with DESeq2 Assembly: GRCz10 Supplementary files format and content: Tab delimited text file with gene Ids and their respective counts,brain/telencephali,,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,tissue:brain/telencephali|genotype:tgher4:RFP low|age:3 mpf|nsc status:Quiescent low expression of her4.3|condition:L|replicate:r12,GSM7668464,GSM7668464: Experiment 12 tgher4:RFP low; Danio rerio; RNA Seq,GSM7668464 r1,GSM7668464,1,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP452071,,,12RL.fastq.gz,fastq,1694665088.0,26479142.0,GSM7668464 r1,0:64,A:412504613;C:441115914;G:486407671;T:354625248;N:11642,64,,,,412504613,441115914,486407671,354625248,11642,SRX21186682,SRS18446703,SRA1683289,Institut Pasteur,Institut Pasteur,1,0.86636,,0.30016,,0.75848,,0.58214,,64,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,France,2023-07-28,Adult,Adult,Brain,Nervous System 77306,SRR25453759,SRX21186681,SRS18446702,SRP452071,PRJNA999746,Transcriptomic differences between deeply quiescent and activated adult NSCs,GSE239594,Transcriptome Analysis,To identify pathways regulating NSC quiescence with a possible link to quiescence depth we used double transgenic Tgher4:drfp;Tgmcm5:gfp fish and paradigms predicted to highlight deep vs shallower quiescence. In adult fish 3 mpf mpf we performed bulk RNA sequencing on FACS sorted RFPhigh GFPneg qNSCs expressing strongly her4 signing NSCs transcriptionally remote from activation and activated NSCs. Overall design: To investigate transcriptomic differences between adult deeply quiescent NSCs and activated NSCs we performed bulk RNA Seq,parent bioproject:PRJNA999741,pubmed:38518783,,Experiment 12 tgher4:RFP high,GSM7668463,,source name:brain/telencephali|tissue:brain/telencephali|genotype:tgher4:RFP high|age:3 mpf|nsc status:Quiescent highly expressing her4.3|condition:H|replicate:r12|geo loc name:missing|collection date:missing,Experiment 12 tgher4:RFP high,Reads were mapped to zebrafish genome using STAR Gene counts were computed using featureCounts Differential expression analysis was performed with DESeq2 Assembly: GRCz10 Supplementary files format and content: Tab delimited text file with gene Ids and their respective counts,brain/telencephali,,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,tissue:brain/telencephali|genotype:tgher4:RFP high|age:3 mpf|nsc status:Quiescent highly expressing her4.3|condition:H|replicate:r12,GSM7668463,GSM7668463: Experiment 12 tgher4:RFP high; Danio rerio; RNA Seq,GSM7668463 r1,GSM7668463,1,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP452071,,,12RH.fastq.gz,fastq,1181540480.0,18461570.0,GSM7668463 r1,0:64,A:282401507;C:312999760;G:348583745;T:237547841;N:7627,64,,,,282401507,312999760,348583745,237547841,7627,SRX21186681,SRS18446702,SRA1683289,Institut Pasteur,Institut Pasteur,1,0.86517,,0.31019,,0.78129,,0.70875,,64,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,France,2023-07-28,Adult,Adult,Brain,Nervous System 77307,SRR25453761,SRX21186679,SRS18446700,SRP452071,PRJNA999746,Transcriptomic differences between deeply quiescent and activated adult NSCs,GSE239594,Transcriptome Analysis,To identify pathways regulating NSC quiescence with a possible link to quiescence depth we used double transgenic Tgher4:drfp;Tgmcm5:gfp fish and paradigms predicted to highlight deep vs shallower quiescence. In adult fish 3 mpf mpf we performed bulk RNA sequencing on FACS sorted RFPhigh GFPneg qNSCs expressing strongly her4 signing NSCs transcriptionally remote from activation and activated NSCs. Overall design: To investigate transcriptomic differences between adult deeply quiescent NSCs and activated NSCs we performed bulk RNA Seq,parent bioproject:PRJNA999741,pubmed:38518783,,Experiment 11 tgher4:RFP low,GSM7668461,,source name:brain/telencephali|tissue:brain/telencephali|genotype:tgher4:RFP low|age:3 mpf|nsc status:Quiescent low expression of her4.3|condition:L|replicate:r11|geo loc name:missing|collection date:missing,Experiment 11 tgher4:RFP low,Reads were mapped to zebrafish genome using STAR Gene counts were computed using featureCounts Differential expression analysis was performed with DESeq2 Assembly: GRCz10 Supplementary files format and content: Tab delimited text file with gene Ids and their respective counts,brain/telencephali,,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,tissue:brain/telencephali|genotype:tgher4:RFP low|age:3 mpf|nsc status:Quiescent low expression of her4.3|condition:L|replicate:r11,GSM7668461,GSM7668461: Experiment 11 tgher4:RFP low; Danio rerio; RNA Seq,GSM7668461 r1,GSM7668461,1,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP452071,,,11RL.fastq.gz,fastq,2358656.0,36854.0,GSM7668461 r1,0:64,A:628520;C:555799;G:609693;T:564639;N:5,64,,,,628520,555799,609693,564639,5,SRX21186679,SRS18446700,SRA1683289,Institut Pasteur,Institut Pasteur,1,0.82276,,0.41018,,0.90621,,0.63658,,64,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,France,2023-07-28,Adult,Adult,Brain,Nervous System 77308,SRR25453762,SRX21186678,SRS18446699,SRP452071,PRJNA999746,Transcriptomic differences between deeply quiescent and activated adult NSCs,GSE239594,Transcriptome Analysis,To identify pathways regulating NSC quiescence with a possible link to quiescence depth we used double transgenic Tgher4:drfp;Tgmcm5:gfp fish and paradigms predicted to highlight deep vs shallower quiescence. In adult fish 3 mpf mpf we performed bulk RNA sequencing on FACS sorted RFPhigh GFPneg qNSCs expressing strongly her4 signing NSCs transcriptionally remote from activation and activated NSCs. Overall design: To investigate transcriptomic differences between adult deeply quiescent NSCs and activated NSCs we performed bulk RNA Seq,parent bioproject:PRJNA999741,pubmed:38518783,,Experiment 11 tgher4:RFP high,GSM7668460,,source name:brain/telencephali|tissue:brain/telencephali|genotype:tgher4:RFP high|age:3 mpf|nsc status:Quiescent highly expressing her4.3|condition:H|replicate:r11|geo loc name:missing|collection date:missing,Experiment 11 tgher4:RFP high,Reads were mapped to zebrafish genome using STAR Gene counts were computed using featureCounts Differential expression analysis was performed with DESeq2 Assembly: GRCz10 Supplementary files format and content: Tab delimited text file with gene Ids and their respective counts,brain/telencephali,,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,tissue:brain/telencephali|genotype:tgher4:RFP high|age:3 mpf|nsc status:Quiescent highly expressing her4.3|condition:H|replicate:r11,GSM7668460,GSM7668460: Experiment 11 tgher4:RFP high; Danio rerio; RNA Seq,GSM7668460 r1,GSM7668460,1,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP452071,,,11RH.fastq.gz,fastq,561279168.0,8769987.0,GSM7668460 r1,0:64,A:138194739;C:146880621;G:155990407;T:120209501;N:3900,64,,,,138194739,146880621,155990407,120209501,3900,SRX21186678,SRS18446699,SRA1683289,Institut Pasteur,Institut Pasteur,1,0.86976,,0.36642,,0.74959,,0.65797,,64,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,France,2023-07-28,Adult,Adult,Brain,Nervous System 77309,SRR25453764,SRX21186676,SRS18446697,SRP452071,PRJNA999746,Transcriptomic differences between deeply quiescent and activated adult NSCs,GSE239594,Transcriptome Analysis,To identify pathways regulating NSC quiescence with a possible link to quiescence depth we used double transgenic Tgher4:drfp;Tgmcm5:gfp fish and paradigms predicted to highlight deep vs shallower quiescence. In adult fish 3 mpf mpf we performed bulk RNA sequencing on FACS sorted RFPhigh GFPneg qNSCs expressing strongly her4 signing NSCs transcriptionally remote from activation and activated NSCs. Overall design: To investigate transcriptomic differences between adult deeply quiescent NSCs and activated NSCs we performed bulk RNA Seq,parent bioproject:PRJNA999741,pubmed:38518783,,Experiment 10 tgher4:RFP low,GSM7668458,,source name:brain/telencephali|tissue:brain/telencephali|genotype:tgher4:RFP low|age:3 mpf|nsc status:Quiescent low expression of her4.3|condition:L|replicate:r10|geo loc name:missing|collection date:missing,Experiment 10 tgher4:RFP low,Reads were mapped to zebrafish genome using STAR Gene counts were computed using featureCounts Differential expression analysis was performed with DESeq2 Assembly: GRCz10 Supplementary files format and content: Tab delimited text file with gene Ids and their respective counts,brain/telencephali,,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,tissue:brain/telencephali|genotype:tgher4:RFP low|age:3 mpf|nsc status:Quiescent low expression of her4.3|condition:L|replicate:r10,GSM7668458,GSM7668458: Experiment 10 tgher4:RFP low; Danio rerio; RNA Seq,GSM7668458 r1,GSM7668458,1,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP452071,,,10RL.fastq.gz,fastq,1007185216.0,15737269.0,GSM7668458 r1,0:64,A:243406379;C:261239943;G:302385706;T:200146973;N:6215,64,,,,243406379,261239943,302385706,200146973,6215,SRX21186676,SRS18446697,SRA1683289,Institut Pasteur,Institut Pasteur,1,0.86856,,0.26032,,0.78892,,0.71216,,64,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,France,2023-07-28,Adult,Adult,Brain,Nervous System 77310,SRR25453765,SRX21186675,SRS18446696,SRP452071,PRJNA999746,Transcriptomic differences between deeply quiescent and activated adult NSCs,GSE239594,Transcriptome Analysis,To identify pathways regulating NSC quiescence with a possible link to quiescence depth we used double transgenic Tgher4:drfp;Tgmcm5:gfp fish and paradigms predicted to highlight deep vs shallower quiescence. In adult fish 3 mpf mpf we performed bulk RNA sequencing on FACS sorted RFPhigh GFPneg qNSCs expressing strongly her4 signing NSCs transcriptionally remote from activation and activated NSCs. Overall design: To investigate transcriptomic differences between adult deeply quiescent NSCs and activated NSCs we performed bulk RNA Seq,parent bioproject:PRJNA999741,pubmed:38518783,,Experiment 10 tgher4:RFP high,GSM7668457,,source name:brain/telencephali|tissue:brain/telencephali|genotype:tgher4:RFP high|age:3 mpf|nsc status:Quiescent highly expressing her4.3|condition:H|replicate:r10|geo loc name:missing|collection date:missing,Experiment 10 tgher4:RFP high,Reads were mapped to zebrafish genome using STAR Gene counts were computed using featureCounts Differential expression analysis was performed with DESeq2 Assembly: GRCz10 Supplementary files format and content: Tab delimited text file with gene Ids and their respective counts,brain/telencephali,,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,tissue:brain/telencephali|genotype:tgher4:RFP high|age:3 mpf|nsc status:Quiescent highly expressing her4.3|condition:H|replicate:r10,GSM7668457,GSM7668457: Experiment 10 tgher4:RFP high; Danio rerio; RNA Seq,GSM7668457 r1,GSM7668457,1,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP452071,,,10RH.fastq.gz,fastq,1086843776.0,16981934.0,GSM7668457 r1,0:64,A:256170266;C:286682618;G:326964274;T:217019550;N:7068,64,,,,256170266,286682618,326964274,217019550,7068,SRX21186675,SRS18446696,SRA1683289,Institut Pasteur,Institut Pasteur,1,0.89673,,0.25794,,0.78281,,0.67305,,64,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,France,2023-07-28,Adult,Adult,Brain,Nervous System 77311,SRR25453757,SRX21186683,SRS18446704,SRP452071,PRJNA999746,Transcriptomic differences between deeply quiescent and activated adult NSCs,GSE239594,Transcriptome Analysis,To identify pathways regulating NSC quiescence with a possible link to quiescence depth we used double transgenic Tgher4:drfp;Tgmcm5:gfp fish and paradigms predicted to highlight deep vs shallower quiescence. In adult fish 3 mpf mpf we performed bulk RNA sequencing on FACS sorted RFPhigh GFPneg qNSCs expressing strongly her4 signing NSCs transcriptionally remote from activation and activated NSCs. Overall design: To investigate transcriptomic differences between adult deeply quiescent NSCs and activated NSCs we performed bulk RNA Seq,parent bioproject:PRJNA999741,pubmed:38518783,,Experiment 13 tgher4:RFP tgmcm5:gfp,GSM7668465,,source name:brain/telencephali|tissue:brain/telencephali|genotype:tgher4:RFP tgmcm5:gfp|age:3 mpf|nsc status:Activated|condition:G|replicate:r13|geo loc name:missing|collection date:missing,Experiment 13 tgher4:RFP tgmcm5:gfp,Reads were mapped to zebrafish genome using STAR Gene counts were computed using featureCounts Differential expression analysis was performed with DESeq2 Assembly: GRCz10 Supplementary files format and content: Tab delimited text file with gene Ids and their respective counts,brain/telencephali,,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,tissue:brain/telencephali|genotype:tgher4:RFP tgmcm5:gfp|age:3 mpf|nsc status:Activated|condition:G|replicate:r13,GSM7668465,GSM7668465: Experiment 13 tgher4:RFP tgmcm5:gfp; Danio rerio; RNA Seq,GSM7668465 r1,GSM7668465,1,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP452071,,,13RG.fastq.gz,fastq,387535808.0,6055247.0,GSM7668465 r1,0:64,A:94655944;C:99109692;G:113770594;T:79997029;N:2549,64,,,,94655944,99109692,113770594,79997029,2549,SRX21186683,SRS18446704,SRA1682601,Institut Pasteur,Institut Pasteur,1,0.87637,,0.29329,,0.7877,,0.59532,,64,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,France,2023-07-28,Adult,Adult,Brain,Nervous System 77312,SRR25453760,SRX21186680,SRS18446701,SRP452071,PRJNA999746,Transcriptomic differences between deeply quiescent and activated adult NSCs,GSE239594,Transcriptome Analysis,To identify pathways regulating NSC quiescence with a possible link to quiescence depth we used double transgenic Tgher4:drfp;Tgmcm5:gfp fish and paradigms predicted to highlight deep vs shallower quiescence. In adult fish 3 mpf mpf we performed bulk RNA sequencing on FACS sorted RFPhigh GFPneg qNSCs expressing strongly her4 signing NSCs transcriptionally remote from activation and activated NSCs. Overall design: To investigate transcriptomic differences between adult deeply quiescent NSCs and activated NSCs we performed bulk RNA Seq,parent bioproject:PRJNA999741,pubmed:38518783,,Experiment 12 tgher4:RFP tgmcm5:gfp,GSM7668462,,source name:brain/telencephali|tissue:brain/telencephali|genotype:tgher4:RFP tgmcm5:gfp|age:3 mpf|nsc status:Activated|condition:G|replicate:r12|geo loc name:missing|collection date:missing,Experiment 12 tgher4:RFP tgmcm5:gfp,Reads were mapped to zebrafish genome using STAR Gene counts were computed using featureCounts Differential expression analysis was performed with DESeq2 Assembly: GRCz10 Supplementary files format and content: Tab delimited text file with gene Ids and their respective counts,brain/telencephali,,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,tissue:brain/telencephali|genotype:tgher4:RFP tgmcm5:gfp|age:3 mpf|nsc status:Activated|condition:G|replicate:r12,GSM7668462,GSM7668462: Experiment 12 tgher4:RFP tgmcm5:gfp; Danio rerio; RNA Seq,GSM7668462 r1,GSM7668462,1,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP452071,,,12RG.fastq.gz,fastq,1740870592.0,27201103.0,GSM7668462 r1,0:64,A:415787017;C:459034090;G:503793126;T:362245237;N:11122,64,,,,415787017,459034090,503793126,362245237,11122,SRX21186680,SRS18446701,SRA1682601,Institut Pasteur,Institut Pasteur,1,0.89438,,0.32229,,0.75237,,0.62254,,64,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,France,2023-07-28,Adult,Adult,Brain,Nervous System 77313,SRR25453763,SRX21186677,SRS18446698,SRP452071,PRJNA999746,Transcriptomic differences between deeply quiescent and activated adult NSCs,GSE239594,Transcriptome Analysis,To identify pathways regulating NSC quiescence with a possible link to quiescence depth we used double transgenic Tgher4:drfp;Tgmcm5:gfp fish and paradigms predicted to highlight deep vs shallower quiescence. In adult fish 3 mpf mpf we performed bulk RNA sequencing on FACS sorted RFPhigh GFPneg qNSCs expressing strongly her4 signing NSCs transcriptionally remote from activation and activated NSCs. Overall design: To investigate transcriptomic differences between adult deeply quiescent NSCs and activated NSCs we performed bulk RNA Seq,parent bioproject:PRJNA999741,pubmed:38518783,,Experiment 11 tgher4:RFP tgmcm5:gfp,GSM7668459,,source name:brain/telencephali|tissue:brain/telencephali|genotype:tgher4:RFP tgmcm5:gfp|age:3 mpf|nsc status:Activated|condition:G|replicate:r11|geo loc name:missing|collection date:missing,Experiment 11 tgher4:RFP tgmcm5:gfp,Reads were mapped to zebrafish genome using STAR Gene counts were computed using featureCounts Differential expression analysis was performed with DESeq2 Assembly: GRCz10 Supplementary files format and content: Tab delimited text file with gene Ids and their respective counts,brain/telencephali,,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,tissue:brain/telencephali|genotype:tgher4:RFP tgmcm5:gfp|age:3 mpf|nsc status:Activated|condition:G|replicate:r11,GSM7668459,GSM7668459: Experiment 11 tgher4:RFP tgmcm5:gfp; Danio rerio; RNA Seq,GSM7668459 r1,GSM7668459,1,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP452071,,,11RG.fastq.gz,fastq,1737498752.0,27148418.0,GSM7668459 r1,0:64,A:426360365;C:450684665;G:510478050;T:349965057;N:10615,64,,,,426360365,450684665,510478050,349965057,10615,SRX21186677,SRS18446698,SRA1682601,Institut Pasteur,Institut Pasteur,1,0.87908,,0.28378,,0.77163,,0.69575,,64,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,France,2023-07-28,Adult,Adult,Brain,Nervous System 77314,SRR25453766,SRX21186674,SRS18446695,SRP452071,PRJNA999746,Transcriptomic differences between deeply quiescent and activated adult NSCs,GSE239594,Transcriptome Analysis,To identify pathways regulating NSC quiescence with a possible link to quiescence depth we used double transgenic Tgher4:drfp;Tgmcm5:gfp fish and paradigms predicted to highlight deep vs shallower quiescence. In adult fish 3 mpf mpf we performed bulk RNA sequencing on FACS sorted RFPhigh GFPneg qNSCs expressing strongly her4 signing NSCs transcriptionally remote from activation and activated NSCs. Overall design: To investigate transcriptomic differences between adult deeply quiescent NSCs and activated NSCs we performed bulk RNA Seq,parent bioproject:PRJNA999741,pubmed:38518783,,Experiment 10 tgher4:RFP tgmcm5:gfp,GSM7668456,,source name:brain/telencephali|tissue:brain/telencephali|genotype:tgher4:RFP tgmcm5:gfp|age:3 mpf|nsc status:Activated|condition:G|replicate:r10|geo loc name:missing|collection date:missing,Experiment 10 tgher4:RFP tgmcm5:gfp,Reads were mapped to zebrafish genome using STAR Gene counts were computed using featureCounts Differential expression analysis was performed with DESeq2 Assembly: GRCz10 Supplementary files format and content: Tab delimited text file with gene Ids and their respective counts,brain/telencephali,,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,tissue:brain/telencephali|genotype:tgher4:RFP tgmcm5:gfp|age:3 mpf|nsc status:Activated|condition:G|replicate:r10,GSM7668456,GSM7668456: Experiment 10 tgher4:RFP tgmcm5:gfp; Danio rerio; RNA Seq,GSM7668456 r1,GSM7668456,1,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP452071,,,10RG.fastq.gz,fastq,1331151616.0,20799244.0,GSM7668456 r1,0:64,A:310326669;C:355505465;G:405609592;T:259699955;N:9935,64,,,,310326669,355505465,405609592,259699955,9935,SRX21186674,SRS18446695,SRA1682601,Institut Pasteur,Institut Pasteur,1,0.8952,,0.2601,,0.7769,,0.6903,,64,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,France,2023-07-28,Adult,Adult,Brain,Nervous System 77315,SRR25453690,SRX21186620,SRS18446641,SRP452067,PRJNA999747,Transcriptomic differences between juvenile and adult quiescent NSCs,GSE239597,Transcriptome Analysis,We generated a dataset in which we compared the bulk transcriptome of qNSCs between 1.5 and 3.5 mpf fish stages between which deeper quiescence is progressively instated in order to find differences between deeply and shallow quiescent NSC Overall design: To investigate transcriptomic differences between adult deeply quiescent NSCs and activated NSCs we performed bulk RNA Seq,parent bioproject:PRJNA999741,pubmed:38518783,,Experiment 8 tgher4:RFP tgmcm5:gfp,GSM7668494,,source name:brain/telencephali|tissue:brain/telencephali|genotype:tgher4:RFP tgmcm5:gfp|nsc status:Activated|cell type:RG|region:tel|age:35m|replicate:r8|geo loc name:missing|collection date:missing,Experiment 8 tgher4:RFP tgmcm5:gfp,Reads were mapped to zebrafish genome using STAR Gene counts were computed using featureCounts Differential expression analysis was performed with DESeq2 Assembly: GRCz11 Supplementary files format and content: Tab delimited text file generated by featureCounts,brain/telencephali,,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,tissue:brain/telencephali|genotype:tgher4:RFP tgmcm5:gfp|nsc status:Activated|cell type:RG|region:tel|age:35m|replicate:r8,GSM7668494,GSM7668494: Experiment 8 tgher4:RFP tgmcm5:gfp; Danio rerio; RNA Seq,GSM7668494 r1,GSM7668494,1,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP452067,,,8R_TCCGGAGA_L007_R1_001.fastq.gz,fastq,1990069575.0,30616455.0,GSM7668494 r1,0:65,A:473644843;C:520846698;G:589102396;T:406389632;N:86006,65,,,,473644843,520846698,589102396,406389632,86006,SRX21186620,SRS18446641,SRA1682605,Institut Pasteur,Institut Pasteur,1,0.91227,,0.28593,,0.77626,,0.66476,,65,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,France,2023-07-28,Undetermined,Multi-stage,Brain,Nervous System 77316,SRR25453691,SRX21186619,SRS18446640,SRP452067,PRJNA999747,Transcriptomic differences between juvenile and adult quiescent NSCs,GSE239597,Transcriptome Analysis,We generated a dataset in which we compared the bulk transcriptome of qNSCs between 1.5 and 3.5 mpf fish stages between which deeper quiescence is progressively instated in order to find differences between deeply and shallow quiescent NSC Overall design: To investigate transcriptomic differences between adult deeply quiescent NSCs and activated NSCs we performed bulk RNA Seq,parent bioproject:PRJNA999741,pubmed:38518783,,Experiment 8 tgher4:RFP,GSM7668493,,source name:brain/telencephali|tissue:brain/telencephali|genotype:tgher4:RFP|nsc status:Quiescent|cell type:R|region:tel|age:35m|replicate:r8|geo loc name:missing|collection date:missing,Experiment 8 tgher4:RFP,Reads were mapped to zebrafish genome using STAR Gene counts were computed using featureCounts Differential expression analysis was performed with DESeq2 Assembly: GRCz11 Supplementary files format and content: Tab delimited text file generated by featureCounts,brain/telencephali,,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,tissue:brain/telencephali|genotype:tgher4:RFP|nsc status:Quiescent|cell type:R|region:tel|age:35m|replicate:r8,GSM7668493,GSM7668493: Experiment 8 tgher4:RFP; Danio rerio; RNA Seq,GSM7668493 r1,GSM7668493,1,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP452067,,,8RG_TCCGCGAA_L007_R1_001.fastq.gz,fastq,2383865380.0,36674852.0,GSM7668493 r1,0:65,A:573283048;C:622540836;G:710185489;T:477753498;N:102509,65,,,,573283048,622540836,710185489,477753498,102509,SRX21186619,SRS18446640,SRA1682605,Institut Pasteur,Institut Pasteur,1,0.90938,,0.2843,,0.76915,,0.66891,,65,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,France,2023-07-28,Undetermined,Multi-stage,Brain,Nervous System 77317,SRR25453692,SRX21186618,SRS18446639,SRP452067,PRJNA999747,Transcriptomic differences between juvenile and adult quiescent NSCs,GSE239597,Transcriptome Analysis,We generated a dataset in which we compared the bulk transcriptome of qNSCs between 1.5 and 3.5 mpf fish stages between which deeper quiescence is progressively instated in order to find differences between deeply and shallow quiescent NSC Overall design: To investigate transcriptomic differences between adult deeply quiescent NSCs and activated NSCs we performed bulk RNA Seq,parent bioproject:PRJNA999741,pubmed:38518783,,Experiment 6 tgher4:RFP tgmcm5:gfp,GSM7668492,,source name:brain/telencephali|tissue:brain/telencephali|genotype:tgher4:RFP tgmcm5:gfp|nsc status:Activated|cell type:RG|region:tel|age:35m|replicate:r6|geo loc name:missing|collection date:missing,Experiment 6 tgher4:RFP tgmcm5:gfp,Reads were mapped to zebrafish genome using STAR Gene counts were computed using featureCounts Differential expression analysis was performed with DESeq2 Assembly: GRCz11 Supplementary files format and content: Tab delimited text file generated by featureCounts,brain/telencephali,,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,tissue:brain/telencephali|genotype:tgher4:RFP tgmcm5:gfp|nsc status:Activated|cell type:RG|region:tel|age:35m|replicate:r6,GSM7668492,GSM7668492: Experiment 6 tgher4:RFP tgmcm5:gfp; Danio rerio; RNA Seq,GSM7668492 r1,GSM7668492,1,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP452067,,,6RG_TAATGCGC_L007_R1_001.fastq.gz,fastq,1719033680.0,26446672.0,GSM7668492 r1,0:65,A:439517820;C:424875107;G:481225010;T:373342716;N:73027,65,,,,439517820,424875107,481225010,373342716,73027,SRX21186618,SRS18446639,SRA1682605,Institut Pasteur,Institut Pasteur,1,0.8987,,0.29445,,0.74105,,0.64512,,65,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,France,2023-07-28,Undetermined,Multi-stage,Brain,Nervous System 77318,SRR25453693,SRX21186617,SRS18446638,SRP452067,PRJNA999747,Transcriptomic differences between juvenile and adult quiescent NSCs,GSE239597,Transcriptome Analysis,We generated a dataset in which we compared the bulk transcriptome of qNSCs between 1.5 and 3.5 mpf fish stages between which deeper quiescence is progressively instated in order to find differences between deeply and shallow quiescent NSC Overall design: To investigate transcriptomic differences between adult deeply quiescent NSCs and activated NSCs we performed bulk RNA Seq,parent bioproject:PRJNA999741,pubmed:38518783,,Experiment 6 tgher4:RFP,GSM7668491,,source name:brain/telencephali|tissue:brain/telencephali|genotype:tgher4:RFP|nsc status:Quiescent|cell type:R|region:tel|age:35m|replicate:r6|geo loc name:missing|collection date:missing,Experiment 6 tgher4:RFP,Reads were mapped to zebrafish genome using STAR Gene counts were computed using featureCounts Differential expression analysis was performed with DESeq2 Assembly: GRCz11 Supplementary files format and content: Tab delimited text file generated by featureCounts,brain/telencephali,,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,tissue:brain/telencephali|genotype:tgher4:RFP|nsc status:Quiescent|cell type:R|region:tel|age:35m|replicate:r6,GSM7668491,GSM7668491: Experiment 6 tgher4:RFP; Danio rerio; RNA Seq,GSM7668491 r1,GSM7668491,1,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP452067,,,6R_CTGAAGCT_L006_R1_001.fastq.gz,fastq,236401295.0,3636943.0,GSM7668491 r1,0:65,A:57600628;C:60492858;G:68869661;T:49424175;N:13973,65,,,,57600628,60492858,68869661,49424175,13973,SRX21186617,SRS18446638,SRA1682605,Institut Pasteur,Institut Pasteur,1,0.90441,,0.28658,,0.76333,,0.68176,,65,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,France,2023-07-28,Undetermined,Multi-stage,Brain,Nervous System 77319,SRR25453694,SRX21186616,SRS18446637,SRP452067,PRJNA999747,Transcriptomic differences between juvenile and adult quiescent NSCs,GSE239597,Transcriptome Analysis,We generated a dataset in which we compared the bulk transcriptome of qNSCs between 1.5 and 3.5 mpf fish stages between which deeper quiescence is progressively instated in order to find differences between deeply and shallow quiescent NSC Overall design: To investigate transcriptomic differences between adult deeply quiescent NSCs and activated NSCs we performed bulk RNA Seq,parent bioproject:PRJNA999741,pubmed:38518783,,Experiment 4 tgher4:RFP tgmcm5:gfp,GSM7668490,,source name:brain/telencephali|tissue:brain/telencephali|genotype:tgher4:RFP tgmcm5:gfp|nsc status:Activated|cell type:RG|region:tel|age:35m|replicate:r4|geo loc name:missing|collection date:missing,Experiment 4 tgher4:RFP tgmcm5:gfp,Reads were mapped to zebrafish genome using STAR Gene counts were computed using featureCounts Differential expression analysis was performed with DESeq2 Assembly: GRCz11 Supplementary files format and content: Tab delimited text file generated by featureCounts,brain/telencephali,,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,tissue:brain/telencephali|genotype:tgher4:RFP tgmcm5:gfp|nsc status:Activated|cell type:RG|region:tel|age:35m|replicate:r4,GSM7668490,GSM7668490: Experiment 4 tgher4:RFP tgmcm5:gfp; Danio rerio; RNA Seq,GSM7668490 r1,GSM7668490,1,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP452067,,,4RG_ATTCAGAA_L006_R1_001.fastq.gz,fastq,2585576630.0,39778102.0,GSM7668490 r1,0:65,A:647806248;C:654823875;G:732496526;T:550295882;N:154099,65,,,,647806248,654823875,732496526,550295882,154099,SRX21186616,SRS18446637,SRA1682605,Institut Pasteur,Institut Pasteur,1,0.89778,,0.34388,,0.74548,,0.61074,,65,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,France,2023-07-28,Undetermined,Multi-stage,Brain,Nervous System 77320,SRR25453695,SRX21186615,SRS18446636,SRP452067,PRJNA999747,Transcriptomic differences between juvenile and adult quiescent NSCs,GSE239597,Transcriptome Analysis,We generated a dataset in which we compared the bulk transcriptome of qNSCs between 1.5 and 3.5 mpf fish stages between which deeper quiescence is progressively instated in order to find differences between deeply and shallow quiescent NSC Overall design: To investigate transcriptomic differences between adult deeply quiescent NSCs and activated NSCs we performed bulk RNA Seq,parent bioproject:PRJNA999741,pubmed:38518783,,Experiment 4 tgher4:RFP,GSM7668489,,source name:brain/telencephali|tissue:brain/telencephali|genotype:tgher4:RFP|nsc status:Quiescent|cell type:R|region:tel|age:35m|replicate:r4|geo loc name:missing|collection date:missing,Experiment 4 tgher4:RFP,Reads were mapped to zebrafish genome using STAR Gene counts were computed using featureCounts Differential expression analysis was performed with DESeq2 Assembly: GRCz11 Supplementary files format and content: Tab delimited text file generated by featureCounts,brain/telencephali,,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,tissue:brain/telencephali|genotype:tgher4:RFP|nsc status:Quiescent|cell type:R|region:tel|age:35m|replicate:r4,GSM7668489,GSM7668489: Experiment 4 tgher4:RFP; Danio rerio; RNA Seq,GSM7668489 r1,GSM7668489,1,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP452067,,,4R_ATTACTCG_L007_R1_001.fastq.gz,fastq,1488627530.0,22901962.0,GSM7668489 r1,0:65,A:376988405;C:376878521;G:409189318;T:325506991;N:64295,65,,,,376988405,376878521,409189318,325506991,64295,SRX21186615,SRS18446636,SRA1682605,Institut Pasteur,Institut Pasteur,1,0.88742,,0.41424,,0.72882,,0.65898,,65,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,France,2023-07-28,Undetermined,Multi-stage,Brain,Nervous System 77321,SRR25453696,SRX21186614,SRS18446635,SRP452067,PRJNA999747,Transcriptomic differences between juvenile and adult quiescent NSCs,GSE239597,Transcriptome Analysis,We generated a dataset in which we compared the bulk transcriptome of qNSCs between 1.5 and 3.5 mpf fish stages between which deeper quiescence is progressively instated in order to find differences between deeply and shallow quiescent NSC Overall design: To investigate transcriptomic differences between adult deeply quiescent NSCs and activated NSCs we performed bulk RNA Seq,parent bioproject:PRJNA999741,pubmed:38518783,,Experiment 3 tgher4:RFP tgmcm5:gfp,GSM7668488,,source name:brain/telencephali|tissue:brain/telencephali|genotype:tgher4:RFP tgmcm5:gfp|nsc status:Activated|cell type:RG|region:tel|age:15m|replicate:r3|geo loc name:missing|collection date:missing,Experiment 3 tgher4:RFP tgmcm5:gfp,Reads were mapped to zebrafish genome using STAR Gene counts were computed using featureCounts Differential expression analysis was performed with DESeq2 Assembly: GRCz11 Supplementary files format and content: Tab delimited text file generated by featureCounts,brain/telencephali,,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,tissue:brain/telencephali|genotype:tgher4:RFP tgmcm5:gfp|nsc status:Activated|cell type:RG|region:tel|age:15m|replicate:r3,GSM7668488,GSM7668488: Experiment 3 tgher4:RFP tgmcm5:gfp; Danio rerio; RNA Seq,GSM7668488 r1,GSM7668488,1,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP452067,,,3RG_TCTCGCGC_L008_R1_001.fastq.gz,fastq,2357869150.0,36274910.0,GSM7668488 r1,0:65,A:575608693;C:613034989;G:678568905;T:490543392;N:113171,65,,,,575608693,613034989,678568905,490543392,113171,SRX21186614,SRS18446635,SRA1682605,Institut Pasteur,Institut Pasteur,1,0.90882,,0.3318,,0.76065,,0.66027,,65,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,France,2023-07-28,Undetermined,Multi-stage,Brain,Nervous System 77322,SRR25453697,SRX21186613,SRS18446634,SRP452067,PRJNA999747,Transcriptomic differences between juvenile and adult quiescent NSCs,GSE239597,Transcriptome Analysis,We generated a dataset in which we compared the bulk transcriptome of qNSCs between 1.5 and 3.5 mpf fish stages between which deeper quiescence is progressively instated in order to find differences between deeply and shallow quiescent NSC Overall design: To investigate transcriptomic differences between adult deeply quiescent NSCs and activated NSCs we performed bulk RNA Seq,parent bioproject:PRJNA999741,pubmed:38518783,,Experiment 3 tgher4:RFP,GSM7668487,,source name:brain/telencephali|tissue:brain/telencephali|genotype:tgher4:RFP|nsc status:Quiescent|cell type:R|region:tel|age:15m|replicate:r3|geo loc name:missing|collection date:missing,Experiment 3 tgher4:RFP,Reads were mapped to zebrafish genome using STAR Gene counts were computed using featureCounts Differential expression analysis was performed with DESeq2 Assembly: GRCz11 Supplementary files format and content: Tab delimited text file generated by featureCounts,brain/telencephali,,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,tissue:brain/telencephali|genotype:tgher4:RFP|nsc status:Quiescent|cell type:R|region:tel|age:15m|replicate:r3,GSM7668487,GSM7668487: Experiment 3 tgher4:RFP; Danio rerio; RNA Seq,GSM7668487 r1,GSM7668487,1,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP452067,,,3R_GAATTCGT_L007_R1_001.fastq.gz,fastq,1536622230.0,23640342.0,GSM7668487 r1,0:65,A:400302281;C:383386741;G:418378970;T:334487419;N:66819,65,,,,400302281,383386741,418378970,334487419,66819,SRX21186613,SRS18446634,SRA1682605,Institut Pasteur,Institut Pasteur,1,0.87737,,0.36524,,0.72991,,0.5329,,65,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,France,2023-07-28,Undetermined,Multi-stage,Brain,Nervous System 77323,SRR25453698,SRX21186612,SRS18446633,SRP452067,PRJNA999747,Transcriptomic differences between juvenile and adult quiescent NSCs,GSE239597,Transcriptome Analysis,We generated a dataset in which we compared the bulk transcriptome of qNSCs between 1.5 and 3.5 mpf fish stages between which deeper quiescence is progressively instated in order to find differences between deeply and shallow quiescent NSC Overall design: To investigate transcriptomic differences between adult deeply quiescent NSCs and activated NSCs we performed bulk RNA Seq,parent bioproject:PRJNA999741,pubmed:38518783,,Experiment 2 tgher4:RFP tgmcm5:gfp,GSM7668486,,source name:brain/telencephali|tissue:brain/telencephali|genotype:tgher4:RFP tgmcm5:gfp|nsc status:Activated|cell type:RG|region:tel|age:15m|replicate:r2|geo loc name:missing|collection date:missing,Experiment 2 tgher4:RFP tgmcm5:gfp,Reads were mapped to zebrafish genome using STAR Gene counts were computed using featureCounts Differential expression analysis was performed with DESeq2 Assembly: GRCz11 Supplementary files format and content: Tab delimited text file generated by featureCounts,brain/telencephali,,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,tissue:brain/telencephali|genotype:tgher4:RFP tgmcm5:gfp|nsc status:Activated|cell type:RG|region:tel|age:15m|replicate:r2,GSM7668486,GSM7668486: Experiment 2 tgher4:RFP tgmcm5:gfp; Danio rerio; RNA Seq,GSM7668486 r1,GSM7668486,1,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP452067,,,2RG_CGGCTATG_L006_R1_001.fastq.gz,fastq,2280472155.0,35084187.0,GSM7668486 r1,0:65,A:590717034;C:568277576;G:627592931;T:493748155;N:136459,65,,,,590717034,568277576,627592931,493748155,136459,SRX21186612,SRS18446633,SRA1682605,Institut Pasteur,Institut Pasteur,1,0.89174,,0.35244,,0.7377,,0.54468,,65,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,France,2023-07-28,Undetermined,Multi-stage,Brain,Nervous System 77324,SRR25453699,SRX21186611,SRS18446632,SRP452067,PRJNA999747,Transcriptomic differences between juvenile and adult quiescent NSCs,GSE239597,Transcriptome Analysis,We generated a dataset in which we compared the bulk transcriptome of qNSCs between 1.5 and 3.5 mpf fish stages between which deeper quiescence is progressively instated in order to find differences between deeply and shallow quiescent NSC Overall design: To investigate transcriptomic differences between adult deeply quiescent NSCs and activated NSCs we performed bulk RNA Seq,parent bioproject:PRJNA999741,pubmed:38518783,,Experiment 2 tgher4:RFP,GSM7668485,,source name:brain/telencephali|tissue:brain/telencephali|genotype:tgher4:RFP|nsc status:Quiescent|cell type:R|region:tel|age:15m|replicate:r2|geo loc name:missing|collection date:missing,Experiment 2 tgher4:RFP,Reads were mapped to zebrafish genome using STAR Gene counts were computed using featureCounts Differential expression analysis was performed with DESeq2 Assembly: GRCz11 Supplementary files format and content: Tab delimited text file generated by featureCounts,brain/telencephali,,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,tissue:brain/telencephali|genotype:tgher4:RFP|nsc status:Quiescent|cell type:R|region:tel|age:15m|replicate:r2,GSM7668485,GSM7668485: Experiment 2 tgher4:RFP; Danio rerio; RNA Seq,GSM7668485 r1,GSM7668485,1,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP452067,,,2R_CTGAAGCT_L007_R1_001.fastq.gz,fastq,1604922800.0,24691120.0,GSM7668485 r1,0:65,A:426901347;C:388498454;G:422016147;T:367437097;N:69755,65,,,,426901347,388498454,422016147,367437097,69755,SRX21186611,SRS18446632,SRA1682605,Institut Pasteur,Institut Pasteur,1,0.86923,,0.39157,,0.70922,,0.59495,,65,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,France,2023-07-28,Undetermined,Multi-stage,Brain,Nervous System 77325,SRR25453700,SRX21186610,SRS18446631,SRP452067,PRJNA999747,Transcriptomic differences between juvenile and adult quiescent NSCs,GSE239597,Transcriptome Analysis,We generated a dataset in which we compared the bulk transcriptome of qNSCs between 1.5 and 3.5 mpf fish stages between which deeper quiescence is progressively instated in order to find differences between deeply and shallow quiescent NSC Overall design: To investigate transcriptomic differences between adult deeply quiescent NSCs and activated NSCs we performed bulk RNA Seq,parent bioproject:PRJNA999741,pubmed:38518783,,Experiment 1 tgher4:RFP tgmcm5:gfp,GSM7668484,,source name:brain/telencephali|tissue:brain/telencephali|genotype:tgher4:RFP tgmcm5:gfp|nsc status:Activated|cell type:RG|region:tel|age:15m|replicate:r1|geo loc name:missing|collection date:missing,Experiment 1 tgher4:RFP tgmcm5:gfp,Reads were mapped to zebrafish genome using STAR Gene counts were computed using featureCounts Differential expression analysis was performed with DESeq2 Assembly: GRCz11 Supplementary files format and content: Tab delimited text file generated by featureCounts,brain/telencephali,,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,tissue:brain/telencephali|genotype:tgher4:RFP tgmcm5:gfp|nsc status:Activated|cell type:RG|region:tel|age:15m|replicate:r1,GSM7668484,GSM7668484: Experiment 1 tgher4:RFP tgmcm5:gfp; Danio rerio; RNA Seq,GSM7668484 r1,GSM7668484,1,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP452067,,,1RG_ATTCAGAA_L008_R1_001.fastq.gz,fastq,1334015540.0,20523316.0,GSM7668484 r1,0:65,A:364210162;C:319706046;G:337403959;T:312630966;N:64407,65,,,,364210162,319706046,337403959,312630966,64407,SRX21186610,SRS18446631,SRA1682605,Institut Pasteur,Institut Pasteur,1,0.86068,,0.46442,,0.71334,,0.58989,,65,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,France,2023-07-28,Undetermined,Multi-stage,Brain,Nervous System 77326,SRR25453701,SRX21186609,SRS18446630,SRP452067,PRJNA999747,Transcriptomic differences between juvenile and adult quiescent NSCs,GSE239597,Transcriptome Analysis,We generated a dataset in which we compared the bulk transcriptome of qNSCs between 1.5 and 3.5 mpf fish stages between which deeper quiescence is progressively instated in order to find differences between deeply and shallow quiescent NSC Overall design: To investigate transcriptomic differences between adult deeply quiescent NSCs and activated NSCs we performed bulk RNA Seq,parent bioproject:PRJNA999741,pubmed:38518783,,Experiment 1 tgher4:RFP,GSM7668483,,source name:brain/telencephali|tissue:brain/telencephali|genotype:tgher4:RFP|nsc status:Quiescent|cell type:R|region:tel|age:15m|replicate:r1|geo loc name:missing|collection date:missing,Experiment 1 tgher4:RFP,Reads were mapped to zebrafish genome using STAR Gene counts were computed using featureCounts Differential expression analysis was performed with DESeq2 Assembly: GRCz11 Supplementary files format and content: Tab delimited text file generated by featureCounts,brain/telencephali,,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,tissue:brain/telencephali|genotype:tgher4:RFP|nsc status:Quiescent|cell type:R|region:tel|age:15m|replicate:r1,GSM7668483,GSM7668483: Experiment 1 tgher4:RFP; Danio rerio; RNA Seq,GSM7668483 r1,GSM7668483,1,PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen® SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP452067,,,1R_ATTACTCG_L006_R1_001.fastq.gz,fastq,1185862925.0,18244045.0,GSM7668483 r1,0:65,A:327160336;C:286538557;G:300617329;T:271475361;N:71342,65,,,,327160336,286538557,300617329,271475361,71342,SRX21186609,SRS18446630,SRA1682605,Institut Pasteur,Institut Pasteur,1,0.84976,,0.45737,,0.70721,,0.59678,,65,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,bulk,bulk,,France,2023-07-28,Undetermined,Multi-stage,Brain,Nervous System