{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", technology = \"bulk\" and tissue_curation_coarse = \"Nervous System\"", "rows": [[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.", null, "pubmed:39052000", null, "EGFRviii PI3KCAH1047R mScarlet tumor negative control brain 2", "GSM7866394", null, "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 \u201cdecoy aware\u201d 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\u2019s 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "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, null, null, null, 1894557984, 1627945034, 1550203852, 2009224463, 16765, "SRX22238470", "SRS19292731", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.94543, null, 0.14646, null, 0.68883, null, 0.49451, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "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.", null, "pubmed:39052000", null, "EGFRviii PI3KCAH1047R mScarlet tumor negative control brain 1", "GSM7866393", null, "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 \u201cdecoy aware\u201d 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\u2019s 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "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, null, null, null, 2099360211, 1783653297, 1717681461, 2239858766, 18594, "SRX22238469", "SRS19292730", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.93984, null, 0.1663, null, 0.69033, null, 0.484, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "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.", null, "pubmed:39052000", null, "KRAS PI3KCAH1047R GFP tumor negative control brain", "GSM7866392", null, "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 \u201cdecoy aware\u201d 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\u2019s 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "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, null, null, null, 2650336113, 2354113843, 2276252979, 2884188285, 23500, "SRX22238468", "SRS19292729", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.94271, null, 0.10831, null, 0.68527, null, 0.50207, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "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.", null, "pubmed:39052000", null, "EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 3", "GSM7866391", null, "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 \u201cdecoy aware\u201d 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\u2019s 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "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, null, null, null, 2627522717, 2223655583, 2134761894, 2810751194, 22782, "SRX22238467", "SRS19292728", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.92543, null, 0.1876, null, 0.67308, null, 0.4886, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "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.", null, "pubmed:39052000", null, "EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 2", "GSM7866390", null, "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 \u201cdecoy aware\u201d 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\u2019s 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "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, null, null, null, 2093456023, 1792947580, 1718784421, 2234389453, 18384, "SRX22238466", "SRS19292727", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.93807, null, 0.14978, null, 0.68854, null, 0.47786, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "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.", null, "pubmed:39052000", null, "EGFRviii PI3KCAH1047R mScarlet tumor positive whole brain 1", "GSM7866389", null, "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 \u201cdecoy aware\u201d 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\u2019s 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "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, null, null, null, 2217465507, 1940028683, 1857031218, 2388930530, 19590, "SRX22238465", "SRS19292726", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.94596, null, 0.12916, null, 0.68619, null, 0.4957, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "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.", null, "pubmed:39052000", null, "KRAS PI3KCAH1047R GFP tumor positive whole brain 3", "GSM7866388", null, "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 \u201cdecoy aware\u201d 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\u2019s 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "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, null, null, null, 2040241047, 1721563382, 1666400346, 2180961056, 17619, "SRX22238464", "SRS19292725", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.93555, null, 0.16895, null, 0.68199, null, 0.50032, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "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.", null, "pubmed:39052000", null, "KRAS PI3KCAH1047R GFP tumor positive whole brain 2", "GSM7866387", null, "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 \u201cdecoy aware\u201d 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\u2019s 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "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, null, null, null, 2223763293, 1944013929, 1869828652, 2408947564, 19901, "SRX22238463", "SRS19292724", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.94943, null, 0.11539, null, 0.68428, null, 0.51019, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "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.", null, "pubmed:39052000", null, "KRAS PI3KCAH1047R GFP tumor positive whole brain 1", "GSM7866386", null, "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 \u201cdecoy aware\u201d 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\u2019s 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP468564", null, "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, null, null, null, 1143856405, 993993009, 951829931, 1236519669, 10039, "SRX22238462", "SRS19292723", "SRA1740017", "Hayes Lab, DSCB, Sickkids Research", "Hayes Lab, DSCB, Sickkids Research", 1, 0.94443, null, 0.13057, null, 0.68503, null, 0.50149, null, 101, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "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.", null, "pubmed:29686887", null, "PCB126 BRAIN4 RNA Seq", "GSM2792798", null, "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.", null, "treatment:PCB126|life history stage:Adult", "GSM2792798", "GSM2792798: PCB126 BRAIN4 RNA Seq; Danio rerio; RNA Seq", "GSM2792798", null, "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", null, "SRP118819", null, null, "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, null, null, 389260936, 298336750, 285290157, 402727589, 13076, "SRX3214272", "SRS2539011", "SRA612796", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.90102, null, 0.20673, null, 0.69152, null, 0.51941, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "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.", null, "pubmed:29686887", null, "PCB126 BRAIN3 RNA Seq", "GSM2792797", null, "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.", null, "treatment:PCB126|life history stage:Adult", "GSM2792797", "GSM2792797: PCB126 BRAIN3 RNA Seq; Danio rerio; RNA Seq", "GSM2792797", null, "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", null, "SRP118819", null, null, "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, null, null, 434098364, 333114785, 318943720, 448043305, 13854, "SRX3214271", "SRS2539012", "SRA612796", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.88591, null, 0.19161, null, 0.67967, null, 0.53267, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "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.", null, "pubmed:29686887", null, "PCB126 BRAIN2 RNA Seq", "GSM2792796", null, "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.", null, "treatment:PCB126|life history stage:Adult", "GSM2792796", "GSM2792796: PCB126 BRAIN2 RNA Seq; Danio rerio; RNA Seq", "GSM2792796", null, "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", null, "SRP118819", null, null, "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, null, null, 419506485, 327077186, 314622527, 431420803, 14275, "SRX3214270", "SRS2539009", "SRA612796", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.89327, null, 0.18282, null, 0.68777, null, 0.53375, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "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.", null, "pubmed:29686887", null, "PCB126 BRAIN1 RNA Seq", "GSM2792795", null, "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.", null, "treatment:PCB126|life history stage:Adult", "GSM2792795", "GSM2792795: PCB126 BRAIN1 RNA Seq; Danio rerio; RNA Seq", "GSM2792795", null, "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", null, "SRP118819", null, null, "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, null, null, 425532690, 346041208, 332010797, 436640179, 14702, "SRX3214269", "SRS2539010", "SRA612796", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.8846, null, 0.14495, null, 0.67142, null, 0.51907, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "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.", null, "pubmed:29686887", null, "CONTROL BRAIN4 RNA Seq", "GSM2792794", null, "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.", null, "treatment:DMSO|life history stage:Adult", "GSM2792794", "GSM2792794: CONTROL BRAIN4 RNA Seq; Danio rerio; RNA Seq", "GSM2792794", null, "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", null, "SRP118819", null, null, "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, null, null, 408992269, 323726908, 309480781, 421041726, 13851, "SRX3214268", "SRS2539008", "SRA612796", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.89686, null, 0.19559, null, 0.69871, null, 0.50956, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "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.", null, "pubmed:29686887", null, "CONTROL BRAIN3 RNA Seq", "GSM2792793", null, "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.", null, "treatment:DMSO|life history stage:Adult", "GSM2792793", "GSM2792793: CONTROL BRAIN3 RNA Seq; Danio rerio; RNA Seq", "GSM2792793", null, "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", null, "SRP118819", null, null, "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, null, null, 452040960, 360441413, 344970351, 466800984, 15202, "SRX3214267", "SRS2539124", "SRA612796", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.89974, null, 0.19642, null, 0.6896, null, 0.49428, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "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.", null, "pubmed:29686887", null, "CONTROL BRAIN2 RNA Seq", "GSM2792792", null, "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.", null, "treatment:DMSO|life history stage:Adult", "GSM2792792", "GSM2792792: CONTROL BRAIN2 RNA Seq; Danio rerio; RNA Seq", "GSM2792792", null, "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", null, "SRP118819", null, null, "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, null, null, 480819797, 388942062, 374434527, 495998198, 16094, "SRX3214266", "SRS2539123", "SRA612796", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.91021, null, 0.19053, null, 0.68603, null, 0.4987, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "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.", null, "pubmed:29686887", null, "CONTROL BRAIN1 RNA Seq", "GSM2792791", null, "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.", null, "treatment:DMSO|life history stage:Adult", "GSM2792791", "GSM2792791: CONTROL BRAIN1 RNA Seq; Danio rerio; RNA Seq", "GSM2792791", null, "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", null, "SRP118819", null, null, "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, null, null, 476861764, 381757171, 366051176, 490460394, 16172, "SRX3214265", "SRS2539120", "SRA612796", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.90508, null, 0.18823, null, 0.69607, null, 0.51563, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "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", null, "AB7155", "GSM3963895", null, "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", null, "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}", null, "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", null, "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", null, "SRP216250", null, "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, null, null, null, 331549647, 254056286, 280458785, 273550294, 109255, "SRX6581798", "SRS5147496", "SRA926018", "GEO", "Immunology, Weizmann Institute of Science", 1, 0.90535, null, 0.17532, null, 0.87803, null, 0.67683, null, 69, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc_generic", "bulk", "bulk", null, "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", null, "AB7154", "GSM3963894", null, "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", null, "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}", null, "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", null, "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", null, "SRP216250", null, "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, null, null, null, 337010566, 261723350, 290674768, 271864761, 111164, "SRX6581797", "SRS5147495", "SRA926018", "GEO", "Immunology, Weizmann Institute of Science", 1, 0.89031, null, 0.18199, null, 0.88154, null, 0.67975, null, 69, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc_generic", "bulk", "bulk", null, "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", null, "AB7153", "GSM3963893", null, "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", null, "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}", null, "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", null, "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", null, "SRP216250", null, "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, null, null, null, 320167297, 243538818, 266263775, 258739754, 101386, "SRX6581796", "SRS5147494", "SRA926018", "GEO", "Immunology, Weizmann Institute of Science", 1, 0.89179, null, 0.12861, null, 0.87259, null, 0.63828, null, 69, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc_generic", "bulk", "bulk", null, "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", null, "AB5657", "GSM3963892", null, "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", null, "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}", null, "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", null, "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", null, "SRP216250", null, "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, null, null, null, 89857088, 69771659, 81302142, 90395650, 6010, "SRX6581795", "SRS5147493", "SRA926018", "GEO", "Immunology, Weizmann Institute of Science", 1, 0.88981, null, 0.33973, null, 0.93507, null, 0.6341, null, 69, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc_generic", "bulk", "bulk", null, "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", null, "AB5657", "GSM3963892", null, "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", null, "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}", null, "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", null, "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", null, "SRP216250", null, "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, null, null, null, 223319161, 173475726, 194239433, 205842249, 31548, "SRX6581795", "SRS5147493", "SRA926018", "GEO", "Immunology, Weizmann Institute of Science", 1, 0.8909, null, 0.30223, null, 0.91802, null, 0.65318, null, 69, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc_generic", "bulk", "bulk", null, "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", null, "AB3014", "GSM3963891", null, "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", null, "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}", null, "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", null, "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", null, "SRP216250", null, "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, null, null, null, 546306466, 392206824, 436944803, 478712291, 27346, "SRX6581794", "SRS5147492", "SRA926018", "GEO", "Immunology, Weizmann Institute of Science", 1, 0.90278, null, 0.4347, null, 0.88925, null, 0.64871, null, 66, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc_generic", "bulk", "bulk", null, "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", null, "pubmed:34054419;pubmed:35204047", null, "injured telencephalic hemisphere 3", "GSM4887529", null, "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", null, "Trizol Invitrogen From 1\u00b5g 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.", null, "tissue:telencephalon|treatment:injury", "GSM4887529", "GSM4887529: injured telencephalic hemisphere 3; Danio rerio; RNA Seq", "GSM4887529", null, "1", "Trizol Invitrogen TrueSeq RNA Illumina", "GEO Accession:GSM4887529", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP291443", null, null, "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, null, null, 333355914, 282050013, 361225960, 448164522, 0, "SRX9450941", "SRS7663855", "SRA1155190", "GEO", "UMR1064, Centre de recherche en transplantation et immunologie", 1, 0.92334, null, 0.08864, null, 0.97611, null, 0.54523, null, 22, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "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", null, "pubmed:34054419;pubmed:35204047", null, "injured telencephalic hemisphere 2", "GSM4887528", null, "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", null, "Trizol Invitrogen From 1\u00b5g 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.", null, "tissue:telencephalon|treatment:injury", "GSM4887528", "GSM4887528: injured telencephalic hemisphere 2; Danio rerio; RNA Seq", "GSM4887528", null, "1", "Trizol Invitrogen TrueSeq RNA Illumina", "GEO Accession:GSM4887528", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP291443", null, null, "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, null, null, 349593244, 293016325, 377668555, 471810417, 0, "SRX9450940", "SRS7663854", "SRA1155190", "GEO", "UMR1064, Centre de recherche en transplantation et immunologie", 1, 0.93253, null, 0.08588, null, 0.97666, null, 0.54494, null, 22, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "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", null, "pubmed:34054419;pubmed:35204047", null, "injured telencephalic hemisphere 1", "GSM4887527", null, "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", null, "Trizol Invitrogen From 1\u00b5g 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.", null, "tissue:telencephalon|treatment:injury", "GSM4887527", "GSM4887527: injured telencephalic hemisphere 1; Danio rerio; RNA Seq", "GSM4887527", null, "1", "Trizol Invitrogen TrueSeq RNA Illumina", "GEO Accession:GSM4887527", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP291443", null, null, "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, null, null, 446653242, 378509659, 482923940, 607602368, 0, "SRX9450939", "SRS7663853", "SRA1155190", "GEO", "UMR1064, Centre de recherche en transplantation et immunologie", 1, 0.91949, null, 0.08917, null, 0.97954, null, 0.53009, null, 21, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "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", null, "pubmed:34054419;pubmed:35204047", null, "healthy telencephalic hemisphere 3", "GSM4887526", null, "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", null, "Trizol Invitrogen From 1\u00b5g 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.", null, "tissue:telencephalon|treatment:no treatment", "GSM4887526", "GSM4887526: healthy telencephalic hemisphere 3; Danio rerio; RNA Seq", "GSM4887526", null, "1", "Trizol Invitrogen TrueSeq RNA Illumina", "GEO Accession:GSM4887526", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP291443", null, null, "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, null, null, 75720892, 64438959, 80940855, 102467938, 0, "SRX9450938", "SRS7663852", "SRA1155190", "GEO", "UMR1064, Centre de recherche en transplantation et immunologie", 1, 0.91791, null, 0.08755, null, 0.98054, null, 0.5616, null, 22, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "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", null, "pubmed:34054419;pubmed:35204047", null, "healthy telencephalic hemisphere 2", "GSM4887525", null, "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", null, "Trizol Invitrogen From 1\u00b5g 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.", null, "tissue:telencephalon|treatment:no treatment", "GSM4887525", "GSM4887525: healthy telencephalic hemisphere 2; Danio rerio; RNA Seq", "GSM4887525", null, "1", "Trizol Invitrogen TrueSeq RNA Illumina", "GEO Accession:GSM4887525", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP291443", null, null, "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, null, null, 125553872, 106408524, 133237076, 168053930, 0, "SRX9450937", "SRS7663851", "SRA1155190", "GEO", "UMR1064, Centre de recherche en transplantation et immunologie", 1, 0.92261, null, 0.08906, null, 0.97881, null, 0.55986, null, 21, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "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", null, "pubmed:34054419;pubmed:35204047", null, "healthy telencephalic hemisphere 1", "GSM4887524", null, "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", null, "Trizol Invitrogen From 1\u00b5g 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.", null, "tissue:telencephalon|treatment:no treatment", "GSM4887524", "GSM4887524: healthy telencephalic hemisphere 1; Danio rerio; RNA Seq", "GSM4887524", null, "1", "Trizol Invitrogen TrueSeq RNA Illumina", "GEO Accession:GSM4887524", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP291443", null, null, "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, null, null, 81497309, 69157722, 86472353, 110585893, 0, "SRX9450936", "SRS7663850", "SRA1155190", "GEO", "UMR1064, Centre de recherche en transplantation et immunologie", 1, 0.91979, null, 0.0902, null, 0.96512, null, 0.56094, null, 22, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Canada", "2020-11-06", "Undetermined", "Adult", "Brain", "Nervous System"], [62931, "SRR13447020", "SRX9860256", "SRS8040687", "SRP301982", "PRJNA692493", "Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]", "GSE164943", "Transcriptome Analysis", "mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.", "parent bioproject:PRJNA692492", "pubmed:33609461", null, "Z 14 3 wpi sc 2", "GSM5023609", null, "source name:21 xxx post injury dpi whole bulk spinal cord|tissue:bulk spinal cord|timepoint:21 xxx post injury", "Z 14 3 wpi sc 2", "Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11", "21 xxx post injury dpi whole bulk spinal cord", "Adult zebrafish were subjected to complete spinal cord transection or sham injured control.", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", null, "tissue:bulk spinal cord|timepoint:21 xxx post injury", "GSM5023609", "GSM5023609: Z 14 3 wpi sc 2; Danio rerio; RNA Seq", "GSM5023609", null, "1", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", "GEO Accession:GSM5023609", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP301982", null, null, "run_2941_s_5_withindex_sequence.txt_GGTTTCG.fq.gz", "fastq", 1344754850.0, 26895097.0, "GSM5023609 r1", "0:50 1:0", "A:368949168;C:303436511;G:303863091;T:368250015;N:256065", 50, 0, null, null, 368949168, 303436511, 303863091, 368250015, 256065, "SRX9860256", "SRS8040687", "SRA1184552", "GEO", "Developmental Biology, Washington University", 1, 0.90723, null, 0.15091, null, 0.70701, null, 0.50468, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-01-15", "Adult", "Adult", "Spinal Cord", "Nervous System"], [62932, "SRR13447019", "SRX9860255", "SRS8040686", "SRP301982", "PRJNA692493", "Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]", "GSE164943", "Transcriptome Analysis", "mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.", "parent bioproject:PRJNA692492", "pubmed:33609461", null, "Z 10 3 wpi sc 1", "GSM5023608", null, "source name:21 xxx post injury dpi whole bulk spinal cord|tissue:bulk spinal cord|timepoint:21 xxx post injury", "Z 10 3 wpi sc 1", "Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11", "21 xxx post injury dpi whole bulk spinal cord", "Adult zebrafish were subjected to complete spinal cord transection or sham injured control.", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", null, "tissue:bulk spinal cord|timepoint:21 xxx post injury", "GSM5023608", "GSM5023608: Z 10 3 wpi sc 1; Danio rerio; RNA Seq", "GSM5023608", null, "1", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", "GEO Accession:GSM5023608", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP301982", null, null, "run_2941_s_5_withindex_sequence.txt_GACCGAA.fq.gz", "fastq", 1479770950.0, 29595419.0, "GSM5023608 r1", "0:50 1:0", "A:405566463;C:336370965;G:334352978;T:403198702;N:281842", 50, 0, null, null, 405566463, 336370965, 334352978, 403198702, 281842, "SRX9860255", "SRS8040686", "SRA1184552", "GEO", "Developmental Biology, Washington University", 1, 0.90956, null, 0.14428, null, 0.70666, null, 0.40811, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-01-15", "Adult", "Adult", "Spinal Cord", "Nervous System"], [62933, "SRR13447018", "SRX9860254", "SRS8040685", "SRP301982", "PRJNA692493", "Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]", "GSE164943", "Transcriptome Analysis", "mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.", "parent bioproject:PRJNA692492", "pubmed:33609461", null, "Z 13 10 dpi sc 2", "GSM5023607", null, "source name:10 xxx post injury dpi whole bulk spinal cord|tissue:bulk spinal cord|timepoint:10 xxx post injury", "Z 13 10 dpi sc 2", "Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11", "10 xxx post injury dpi whole bulk spinal cord", "Adult zebrafish were subjected to complete spinal cord transection or sham injured control.", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", null, "tissue:bulk spinal cord|timepoint:10 xxx post injury", "GSM5023607", "GSM5023607: Z 13 10 dpi sc 2; Danio rerio; RNA Seq", "GSM5023607", null, "1", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", "GEO Accession:GSM5023607", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP301982", null, null, "run_2941_s_5_withindex_sequence.txt_TTACCGT.fq.gz", "fastq", 2001230650.0, 40024613.0, "GSM5023607 r1", "0:50 1:0", "A:563937717;C:433011935;G:427243197;T:576659283;N:378518", 50, 0, null, null, 563937717, 433011935, 427243197, 576659283, 378518, "SRX9860254", "SRS8040685", "SRA1184552", "GEO", "Developmental Biology, Washington University", 1, 0.88738, null, 0.25515, null, 0.74576, null, 0.61121, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-01-15", "Adult", "Adult", "Spinal Cord", "Nervous System"], [62934, "SRR13447017", "SRX9860253", "SRS8040684", "SRP301982", "PRJNA692493", "Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]", "GSE164943", "Transcriptome Analysis", "mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.", "parent bioproject:PRJNA692492", "pubmed:33609461", null, "Z 9 10 dpi sc 1", "GSM5023606", null, "source name:10 xxx post injury dpi whole bulk spinal cord|tissue:bulk spinal cord|timepoint:10 xxx post injury", "Z 9 10 dpi sc 1", "Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11", "10 xxx post injury dpi whole bulk spinal cord", "Adult zebrafish were subjected to complete spinal cord transection or sham injured control.", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", null, "tissue:bulk spinal cord|timepoint:10 xxx post injury", "GSM5023606", "GSM5023606: Z 9 10 dpi sc 1; Danio rerio; RNA Seq", "GSM5023606", null, "1", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", "GEO Accession:GSM5023606", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP301982", null, null, "run_2941_s_5_withindex_sequence.txt_TAGGATG.fq.gz", "fastq", 1228530350.0, 24570607.0, "GSM5023606 r1", "0:50 1:0", "A:336797190;C:276687423;G:274112310;T:340700127;N:233300", 50, 0, null, null, 336797190, 276687423, 274112310, 340700127, 233300, "SRX9860253", "SRS8040684", "SRA1184552", "GEO", "Developmental Biology, Washington University", 1, 0.90494, null, 0.17991, null, 0.69789, null, 0.43663, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-01-15", "Adult", "Adult", "Spinal Cord", "Nervous System"], [62935, "SRR13447016", "SRX9860252", "SRS8040683", "SRP301982", "PRJNA692493", "Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]", "GSE164943", "Transcriptome Analysis", "mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.", "parent bioproject:PRJNA692492", "pubmed:33609461", null, "Z 12 5 dpi sc 2", "GSM5023605", null, "source name:5 xxx post injury dpi whole bulk spinal cord|tissue:bulk spinal cord|timepoint:5 xxx post injury", "Z 12 5 dpi sc 2", "Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11", "5 xxx post injury dpi whole bulk spinal cord", "Adult zebrafish were subjected to complete spinal cord transection or sham injured control.", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", null, "tissue:bulk spinal cord|timepoint:5 xxx post injury", "GSM5023605", "GSM5023605: Z 12 5 dpi sc 2; Danio rerio; RNA Seq", "GSM5023605", null, "1", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", "GEO Accession:GSM5023605", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP301982", null, null, "run_2941_s_5_withindex_sequence.txt_CGCCGTA.fq.gz", "fastq", 1304617300.0, 26092346.0, "GSM5023605 r1", "0:50 1:0", "A:354720856;C:300934683;G:299416035;T:349298501;N:247225", 50, 0, null, null, 354720856, 300934683, 299416035, 349298501, 247225, "SRX9860252", "SRS8040683", "SRA1184552", "GEO", "Developmental Biology, Washington University", 1, 0.91217, null, 0.12965, null, 0.69609, null, 0.45367, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-01-15", "Adult", "Adult", "Spinal Cord", "Nervous System"], [62936, "SRR13447015", "SRX9860251", "SRS8040682", "SRP301982", "PRJNA692493", "Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]", "GSE164943", "Transcriptome Analysis", "mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.", "parent bioproject:PRJNA692492", "pubmed:33609461", null, "Z 8 5 dpi sc 1", "GSM5023604", null, "source name:5 xxx post injury dpi whole bulk spinal cord|tissue:bulk spinal cord|timepoint:5 xxx post injury", "Z 8 5 dpi sc 1", "Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11", "5 xxx post injury dpi whole bulk spinal cord", "Adult zebrafish were subjected to complete spinal cord transection or sham injured control.", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", null, "tissue:bulk spinal cord|timepoint:5 xxx post injury", "GSM5023604", "GSM5023604: Z 8 5 dpi sc 1; Danio rerio; RNA Seq", "GSM5023604", null, "1", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", "GEO Accession:GSM5023604", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP301982", null, null, "run_2941_s_5_withindex_sequence.txt_CATACTG.fq.gz", "fastq", 1396287400.0, 27925748.0, "GSM5023604 r1", "0:50 1:0", "A:377321251;C:319668467;G:314347283;T:384684913;N:265486", 50, 0, null, null, 377321251, 319668467, 314347283, 384684913, 265486, "SRX9860251", "SRS8040682", "SRA1184552", "GEO", "Developmental Biology, Washington University", 1, 0.91125, null, 0.14506, null, 0.69777, null, 0.4557, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-01-15", "Adult", "Adult", "Spinal Cord", "Nervous System"], [62937, "SRR13447014", "SRX9860250", "SRS8040681", "SRP301982", "PRJNA692493", "Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]", "GSE164943", "Transcriptome Analysis", "mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.", "parent bioproject:PRJNA692492", "pubmed:33609461", null, "Z 11 uninjured sc 2", "GSM5023603", null, "source name:Bulk uninjured spinal cord|tissue:bulk spinal cord|timepoint:Uninjured", "Z 11 uninjured sc 2", "Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11", "Bulk uninjured spinal cord", "Adult zebrafish were subjected to complete spinal cord transection or sham injured control.", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", null, "tissue:bulk spinal cord|timepoint:Uninjured", "GSM5023603", "GSM5023603: Z 11 uninjured sc 2; Danio rerio; RNA Seq", "GSM5023603", null, "1", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", "GEO Accession:GSM5023603", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP301982", null, null, "run_2941_s_5_withindex_sequence.txt_CGTGATA.fq.gz", "fastq", 1422401500.0, 28448030.0, "GSM5023603 r1", "0:50 1:0", "A:383424800;C:325837613;G:322858241;T:390009650;N:271196", 50, 0, null, null, 383424800, 325837613, 322858241, 390009650, 271196, "SRX9860250", "SRS8040681", "SRA1184552", "GEO", "Developmental Biology, Washington University", 1, 0.918, null, 0.1183, null, 0.7163, null, 0.50669, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-01-15", "Adult", "Adult", "Spinal Cord", "Nervous System"], [62938, "SRR13447013", "SRX9860249", "SRS8040680", "SRP301982", "PRJNA692493", "Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]", "GSE164943", "Transcriptome Analysis", "mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.", "parent bioproject:PRJNA692492", "pubmed:33609461", null, "Z 7 uninjured sc 1", "GSM5023602", null, "source name:Bulk uninjured spinal cord|tissue:bulk spinal cord|timepoint:Uninjured", "Z 7 uninjured sc 1", "Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11", "Bulk uninjured spinal cord", "Adult zebrafish were subjected to complete spinal cord transection or sham injured control.", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", null, "tissue:bulk spinal cord|timepoint:Uninjured", "GSM5023602", "GSM5023602: Z 7 uninjured sc 1; Danio rerio; RNA Seq", "GSM5023602", null, "1", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", "GEO Accession:GSM5023602", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP301982", null, null, "run_2941_s_5_withindex_sequence.txt_CCCGCTA.fq.gz", "fastq", 1274023900.0, 25480478.0, "GSM5023602 r1", "0:50 1:0", "A:330443270;C:305732881;G:301431401;T:336172878;N:243470", 50, 0, null, null, 330443270, 305732881, 301431401, 336172878, 243470, "SRX9860249", "SRS8040680", "SRA1184552", "GEO", "Developmental Biology, Washington University", 1, 0.92713, null, 0.09501, null, 0.71776, null, 0.49328, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-01-15", "Adult", "Adult", "Spinal Cord", "Nervous System"], [62939, "SRR13447012", "SRX9860248", "SRS8040679", "SRP301982", "PRJNA692493", "Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]", "GSE164943", "Transcriptome Analysis", "mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.", "parent bioproject:PRJNA692492", "pubmed:33609461", null, "Z 3 gp rp rna 1", "GSM5023601", null, "source name:FACS sorted ctgfa:mCherry;gfap:EGFP cells|tissue:ctgfa:mCherry;gfap:EGFP cells|timepoint:5 xxx post injury", "Z 3 gp rp rna 1", "Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11", "FACS sorted ctgfa:mCherry;gfap:EGFP cells", "Adult zebrafish were subjected to complete spinal cord transection or sham injured control.", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", null, "tissue:ctgfa:mCherry;gfap:EGFP cells|timepoint:5 xxx post injury", "GSM5023601", "GSM5023601: Z 3 gp rp rna 1; Danio rerio; RNA Seq", "GSM5023601", null, "1", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", "GEO Accession:GSM5023601", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP301982", null, null, "run_2941_s_5_withindex_sequence.txt_ATAGGCT.fq.gz", "fastq", 1480993150.0, 29619863.0, "GSM5023601 r1", "0:50 1:0", "A:407241408;C:335585510;G:332782981;T:405104683;N:278568", 50, 0, null, null, 407241408, 335585510, 332782981, 405104683, 278568, "SRX9860248", "SRS8040679", "SRA1184552", "GEO", "Developmental Biology, Washington University", 1, 0.90012, null, 0.13909, null, 0.75684, null, 0.59867, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-01-15", "Adult", "Adult", "Spinal Cord", "Nervous System"], [62940, "SRR13447011", "SRX9860247", "SRS8040678", "SRP301982", "PRJNA692493", "Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]", "GSE164943", "Transcriptome Analysis", "mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.", "parent bioproject:PRJNA692492", "pubmed:33609461", null, "Z 18 gp rp 3", "GSM5023600", null, "source name:FACS sorted ctgfa:mCherry;gfap:EGFP cells|tissue:ctgfa:mCherry;gfap:EGFP cells|timepoint:5 xxx post injury", "Z 18 gp rp 3", "Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11", "FACS sorted ctgfa:mCherry;gfap:EGFP cells", "Adult zebrafish were subjected to complete spinal cord transection or sham injured control.", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", null, "tissue:ctgfa:mCherry;gfap:EGFP cells|timepoint:5 xxx post injury", "GSM5023600", "GSM5023600: Z 18 gp rp 3; Danio rerio; RNA Seq", "GSM5023600", null, "1", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", "GEO Accession:GSM5023600", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP301982", null, null, "run_2941_s_5_withindex_sequence.txt_AATGACT.fq.gz", "fastq", 1583531750.0, 31670635.0, "GSM5023600 r1", "0:50 1:0", "A:429031314;C:366679713;G:363462738;T:424058514;N:299471", 50, 0, null, null, 429031314, 366679713, 363462738, 424058514, 299471, "SRX9860247", "SRS8040678", "SRA1184552", "GEO", "Developmental Biology, Washington University", 1, 0.90969, null, 0.12671, null, 0.7458, null, 0.57895, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-01-15", "Adult", "Adult", "Spinal Cord", "Nervous System"], [62941, "SRR13447010", "SRX9860246", "SRS8040677", "SRP301982", "PRJNA692493", "Localized EMT reprograms glial progenitors to promote spinal cord repair [bulk RNA seq]", "GSE164943", "Transcriptome Analysis", "mCherry/EGFP double positive cells were isolated from the spinal cords of Tgctgfa:mCherry; gfap:EGFP zebrafish at 5 xxx post injury. Bulk spinal cord tissue at 5 10 and 21 xxx post injury were also sequenced. Overall design: Whole RNA sequencing of FACS sorted ctgfa:mCherry; gfap:EGFP cells and bulk spinal cord tissue.", "parent bioproject:PRJNA692492", "pubmed:33609461", null, "Z 15 gp rp 1", "GSM5023599", null, "source name:FACS sorted ctgfa:mCherry;gfap:EGFP cells|tissue:ctgfa:mCherry;gfap:EGFP cells|timepoint:5 xxx post injury", "Z 15 gp rp 1", "Quality control and trimming of adapters and short sequences using Fastx Sequence reads mapped to the zebrafish genome Zv11 using Bowtie2 Sequence reads assembled and quantified using Cufflinks and Cuffdiff algorithms Genome build: Zv11", "FACS sorted ctgfa:mCherry;gfap:EGFP cells", "Adult zebrafish were subjected to complete spinal cord transection or sham injured control.", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", null, "tissue:ctgfa:mCherry;gfap:EGFP cells|timepoint:5 xxx post injury", "GSM5023599", "GSM5023599: Z 15 gp rp 1; Danio rerio; RNA Seq", "GSM5023599", null, "1", "For FACS seq animals were lesioned and dissociated to set up FACS gates. Tissues were dissociated using 0.05% trypsin for 5 min at room temperature. Cell supernatants were triturated in DMEM with 20% fetal bovine serum and applied to a 100 um cell strainer. Dissociated cells were pelleted resuspended and sorter using a MoFlo cell sorter machine. Total RNA was prepared using a NucleoSpin RNA Plus XS kit according to manufacturer's specifications. TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp single end reads", "GEO Accession:GSM5023599", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP301982", null, null, "run_2941_s_5_withindex_sequence.txt_TTCTTCG.fq.gz", "fastq", 1324698650.0, 26493973.0, "GSM5023599 r1", "0:50 1:0", "A:361437407;C:301526323;G:300125135;T:361356767;N:253018", 50, 0, null, null, 361437407, 301526323, 300125135, 361356767, 253018, "SRX9860246", "SRS8040677", "SRA1184552", "GEO", "Developmental Biology, Washington University", 1, 0.90938, null, 0.14229, null, 0.70869, null, 0.50563, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-01-15", "Adult", "Adult", "Spinal Cord", "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", null, "Experiment 13 tgher4:RFP low", "GSM7668467", null, "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", null, "PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen\u00ae SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories", null, "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\u00ae SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452071", null, null, "13RL.fastq.gz", "fastq", 2089168000.0, 32643250.0, "GSM7668467 r1", "0:64", "A:491435480;C:556848569;G:626704317;T:414165769;N:13865", 64, null, null, null, 491435480, 556848569, 626704317, 414165769, 13865, "SRX21186685", "SRS18446706", "SRA1683289", "Institut Pasteur", "Institut Pasteur", 1, 0.8119, null, 0.23552, null, 0.78575, null, 0.66137, null, 64, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "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", null, "Experiment 13 tgher4:RFP high", "GSM7668466", null, "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", null, "PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen\u00ae SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories", null, "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\u00ae SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452071", null, null, "13RH.fastq.gz", "fastq", 1736530176.0, 27133284.0, "GSM7668466 r1", "0:64", "A:421791163;C:450901073;G:507159612;T:356667757;N:10571", 64, null, null, null, 421791163, 450901073, 507159612, 356667757, 10571, "SRX21186684", "SRS18446705", "SRA1683289", "Institut Pasteur", "Institut Pasteur", 1, 0.86128, null, 0.27411, null, 0.76187, null, 0.61881, null, 64, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "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", null, "Experiment 12 tgher4:RFP low", "GSM7668464", null, "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", null, "PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen\u00ae SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories", null, "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\u00ae SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452071", null, null, "12RL.fastq.gz", "fastq", 1694665088.0, 26479142.0, "GSM7668464 r1", "0:64", "A:412504613;C:441115914;G:486407671;T:354625248;N:11642", 64, null, null, null, 412504613, 441115914, 486407671, 354625248, 11642, "SRX21186682", "SRS18446703", "SRA1683289", "Institut Pasteur", "Institut Pasteur", 1, 0.86636, null, 0.30016, null, 0.75848, null, 0.58214, null, 64, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "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", null, "Experiment 12 tgher4:RFP high", "GSM7668463", null, "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", null, "PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen\u00ae SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories", null, "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\u00ae SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452071", null, null, "12RH.fastq.gz", "fastq", 1181540480.0, 18461570.0, "GSM7668463 r1", "0:64", "A:282401507;C:312999760;G:348583745;T:237547841;N:7627", 64, null, null, null, 282401507, 312999760, 348583745, 237547841, 7627, "SRX21186681", "SRS18446702", "SRA1683289", "Institut Pasteur", "Institut Pasteur", 1, 0.86517, null, 0.31019, null, 0.78129, null, 0.70875, null, 64, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "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", null, "Experiment 11 tgher4:RFP low", "GSM7668461", null, "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", null, "PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen\u00ae SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories", null, "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\u00ae SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452071", null, null, "11RL.fastq.gz", "fastq", 2358656.0, 36854.0, "GSM7668461 r1", "0:64", "A:628520;C:555799;G:609693;T:564639;N:5", 64, null, null, null, 628520, 555799, 609693, 564639, 5, "SRX21186679", "SRS18446700", "SRA1683289", "Institut Pasteur", "Institut Pasteur", 1, 0.82276, null, 0.41018, null, 0.90621, null, 0.63658, null, 64, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "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", null, "Experiment 11 tgher4:RFP high", "GSM7668460", null, "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", null, "PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen\u00ae SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories", null, "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\u00ae SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452071", null, null, "11RH.fastq.gz", "fastq", 561279168.0, 8769987.0, "GSM7668460 r1", "0:64", "A:138194739;C:146880621;G:155990407;T:120209501;N:3900", 64, null, null, null, 138194739, 146880621, 155990407, 120209501, 3900, "SRX21186678", "SRS18446699", "SRA1683289", "Institut Pasteur", "Institut Pasteur", 1, 0.86976, null, 0.36642, null, 0.74959, null, 0.65797, null, 64, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "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", null, "Experiment 10 tgher4:RFP low", "GSM7668458", null, "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", null, "PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen\u00ae SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories", null, "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\u00ae SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452071", null, null, "10RL.fastq.gz", "fastq", 1007185216.0, 15737269.0, "GSM7668458 r1", "0:64", "A:243406379;C:261239943;G:302385706;T:200146973;N:6215", 64, null, null, null, 243406379, 261239943, 302385706, 200146973, 6215, "SRX21186676", "SRS18446697", "SRA1683289", "Institut Pasteur", "Institut Pasteur", 1, 0.86856, null, 0.26032, null, 0.78892, null, 0.71216, null, 64, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "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", null, "Experiment 10 tgher4:RFP high", "GSM7668457", null, "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", null, "PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen\u00ae SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories", null, "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\u00ae SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452071", null, null, "10RH.fastq.gz", "fastq", 1086843776.0, 16981934.0, "GSM7668457 r1", "0:64", "A:256170266;C:286682618;G:326964274;T:217019550;N:7068", 64, null, null, null, 256170266, 286682618, 326964274, 217019550, 7068, "SRX21186675", "SRS18446696", "SRA1683289", "Institut Pasteur", "Institut Pasteur", 1, 0.89673, null, 0.25794, null, 0.78281, null, 0.67305, null, 64, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "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. 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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", null, "Experiment 12 tgher4:RFP tgmcm5:gfp", "GSM7668462", null, "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", null, "PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen\u00ae SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories", null, "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\u00ae SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452071", null, null, "12RG.fastq.gz", "fastq", 1740870592.0, 27201103.0, "GSM7668462 r1", "0:64", "A:415787017;C:459034090;G:503793126;T:362245237;N:11122", 64, null, null, null, 415787017, 459034090, 503793126, 362245237, 11122, "SRX21186680", "SRS18446701", "SRA1682601", "Institut Pasteur", "Institut Pasteur", 1, 0.89438, null, 0.32229, null, 0.75237, null, 0.62254, null, 64, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "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", null, "Experiment 11 tgher4:RFP tgmcm5:gfp", "GSM7668459", null, "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", null, "PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen\u00ae SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories", null, "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\u00ae SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP452071", null, null, "11RG.fastq.gz", "fastq", 1737498752.0, 27148418.0, "GSM7668459 r1", "0:64", "A:426360365;C:450684665;G:510478050;T:349965057;N:10615", 64, null, null, null, 426360365, 450684665, 510478050, 349965057, 10615, "SRX21186677", "SRS18446698", "SRA1682601", "Institut Pasteur", "Institut Pasteur", 1, 0.87908, null, 0.28378, null, 0.77163, null, 0.69575, null, 64, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "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", null, "Experiment 10 tgher4:RFP tgmcm5:gfp", "GSM7668456", null, "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", null, "PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen\u00ae SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories", null, 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"bulk", "bulk", null, "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", null, "Experiment 8 tgher4:RFP tgmcm5:gfp", "GSM7668494", null, "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 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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", null, "Experiment 8 tgher4:RFP", "GSM7668493", null, "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", null, "PicoPure Isolation kit Life technologies RNase free DNase Set Qiagen\u00ae SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian kit Clontech Laboratories", null, 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"smarter", "bulk", "bulk", "bulk", null, "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", null, "Experiment 6 tgher4:RFP tgmcm5:gfp", "GSM7668492", null, "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 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"Illumina HiSeq 2500", null, "SRP452067", null, null, "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, null, null, null, 439517820, 424875107, 481225010, 373342716, 73027, "SRX21186618", "SRS18446639", "SRA1682605", "Institut Pasteur", "Institut Pasteur", 1, 0.8987, null, 0.29445, null, 0.74105, null, 0.64512, null, 65, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "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 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