{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC\", experiment.library_strategy = \"RNA-Seq\" and technology = \"marsseq\"", "rows": [[32806, "SRR29478752", "SRX24989905", "SRS21691708", "SRP515053", "PRJNA1126173", "Endolysosomal dysfunction in radial glia progenitor cells leads to defective cerebral angiogenesis and compromised blood brain barrier integrity", "GSE270309", "Transcriptome Analysis", "The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to severe vascular defects hemorrhages and a leaky BBB. Altogether our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to severe vascular defects hemorrhages and a leaky BBB. Altogether our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to severe vascular defects hemorrhages and a leaky BBB. Altogether our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. Overall design: 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension . Sorting and RNA extraction was performed on TgBACscar2ba:KalTA4; UAS mKate2", null, "pubmed:39289367", null, "head scarb2a mut rep 3", "GSM8339369", null, "source name:head|tissue:head|cell type:scarb2a+ cells|genotype:scarb2a mut|geo loc name:missing|collection date:missing", "head scarb2a mut rep 3", "done using the User friendly Transcriptomic Analysis Pipeline Assembly: danRer11 Supplementary files format and content: countsMatrix normalized.txt: expression dataset txt file contaning normalized UMI counts table for all samples.", "head", null, "For each experimental condition a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche trypsin B BI and DNAseI Roche the cell suspension was strained through a 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation RT and PCR. The final library concentration was measured by Qubit TapeStation and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing and each sample was sequenced for 6M reads.", null, "tissue:head|cell type:scarb2a+ cells|genotype:scarb2a mut", "GSM8339369", "GSM8339369: head scarb2a mut rep 3; Danio rerio; RNA Seq", "GSM8339369 r1", "GSM8339369", "1", "For each experimental condition a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche trypsin B BI and DNAseI Roche the cell suspension was strained through a 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation RT and PCR. The final library concentration was measured by Qubit TapeStation and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing and each sample was sequenced for 6M reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP515053", null, null, "scarb2_mut3_R2.fastq.gz scarb2_mut3_R1.fastq.gz", "fastq fastq", 590803877.0, 7118119.0, "GSM8339369 r1", "0:75 1:8", "A:171152826;C:118382558;G:138973475;T:162287717;N:7301", 75, 8, null, null, 171152826, 118382558, 138973475, 162287717, 7301, "SRX24989905", "SRS21691708", "SRA1904886", "Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science", "Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science", 2, 0.86187, 0.0, 0.06751, 0.0, 0.80081, 1.0, 0.47421, null, 75, 8, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2024-06-20", "Hatching", "Embryo", "Head", "Nervous System"], [32807, "SRR29478753", "SRX24989904", "SRS21691707", "SRP515053", "PRJNA1126173", "Endolysosomal dysfunction in radial glia progenitor cells leads to defective cerebral angiogenesis and compromised blood brain barrier integrity", "GSE270309", "Transcriptome Analysis", "The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to severe vascular defects hemorrhages and a leaky BBB. Altogether our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to severe vascular defects hemorrhages and a leaky BBB. Altogether our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to severe vascular defects hemorrhages and a leaky BBB. Altogether our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. Overall design: 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension . Sorting and RNA extraction was performed on TgBACscar2ba:KalTA4; UAS mKate2", null, "pubmed:39289367", null, "head scarb2a mut rep 2", "GSM8339368", null, "source name:head|tissue:head|cell type:scarb2a+ cells|genotype:scarb2a mut|geo loc name:missing|collection date:missing", "head scarb2a mut rep 2", "done using the User friendly Transcriptomic Analysis Pipeline Assembly: danRer11 Supplementary files format and content: countsMatrix normalized.txt: expression dataset txt file contaning normalized UMI counts table for all samples.", "head", null, "For each experimental condition a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche trypsin B BI and DNAseI Roche the cell suspension was strained through a 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation RT and PCR. The final library concentration was measured by Qubit TapeStation and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing and each sample was sequenced for 6M reads.", null, "tissue:head|cell type:scarb2a+ cells|genotype:scarb2a mut", "GSM8339368", "GSM8339368: head scarb2a mut rep 2; Danio rerio; RNA Seq", "GSM8339368 r1", "GSM8339368", "1", "For each experimental condition a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche trypsin B BI and DNAseI Roche the cell suspension was strained through a 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation RT and PCR. The final library concentration was measured by Qubit TapeStation and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing and each sample was sequenced for 6M reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP515053", null, null, "scarb2_mut2_R2.fastq.gz scarb2_mut2_R1.fastq.gz", "fastq fastq", 560228337.0, 6749739.0, "GSM8339368 r1", "0:75 1:8", "A:161395198;C:113034644;G:131199008;T:154592664;N:6823", 75, 8, null, null, 161395198, 113034644, 131199008, 154592664, 6823, "SRX24989904", "SRS21691707", "SRA1904886", "Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science", "Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science", 2, 0.85633, 0.0, 0.06116, 0.0, 0.80438, 1.0, 0.47226, null, 75, 8, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2024-06-20", "Hatching", "Embryo", "Head", "Nervous System"], [32808, "SRR29478754", "SRX24989903", "SRS21691706", "SRP515053", "PRJNA1126173", "Endolysosomal dysfunction in radial glia progenitor cells leads to defective cerebral angiogenesis and compromised blood brain barrier integrity", "GSE270309", "Transcriptome Analysis", "The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to severe vascular defects hemorrhages and a leaky BBB. Altogether our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to severe vascular defects hemorrhages and a leaky BBB. Altogether our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to severe vascular defects hemorrhages and a leaky BBB. Altogether our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. Overall design: 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension . Sorting and RNA extraction was performed on TgBACscar2ba:KalTA4; UAS mKate2", null, "pubmed:39289367", null, "head scarb2a mut rep 1", "GSM8339367", null, "source name:head|tissue:head|cell type:scarb2a+ cells|genotype:scarb2a mut|geo loc name:missing|collection date:missing", "head scarb2a mut rep 1", "done using the User friendly Transcriptomic Analysis Pipeline Assembly: danRer11 Supplementary files format and content: countsMatrix normalized.txt: expression dataset txt file contaning normalized UMI counts table for all samples.", "head", null, "For each experimental condition a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche trypsin B BI and DNAseI Roche the cell suspension was strained through a 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation RT and PCR. The final library concentration was measured by Qubit TapeStation and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing and each sample was sequenced for 6M reads.", null, "tissue:head|cell type:scarb2a+ cells|genotype:scarb2a mut", "GSM8339367", "GSM8339367: head scarb2a mut rep 1; Danio rerio; RNA Seq", "GSM8339367 r1", "GSM8339367", "1", "For each experimental condition a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche trypsin B BI and DNAseI Roche the cell suspension was strained through a 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation RT and PCR. The final library concentration was measured by Qubit TapeStation and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing and each sample was sequenced for 6M reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP515053", null, null, "scarb2_mut1_R1.fastq.gz scarb2_mut1_R2.fastq.gz", "fastq fastq", 536045042.0, 6458374.0, "GSM8339367 r1", "0:75 1:8", "A:152863781;C:109210501;G:126922310;T:147041910;N:6540", 75, 8, null, null, 152863781, 109210501, 126922310, 147041910, 6540, "SRX24989903", "SRS21691706", "SRA1904886", "Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science", "Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science", 2, 0.86464, 0.0, 0.06577, 0.0, 0.80359, 1.0, 0.48395, null, 75, 8, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2024-06-20", "Hatching", "Embryo", "Head", "Nervous System"], [32809, "SRR29478755", "SRX24989902", "SRS21691705", "SRP515053", "PRJNA1126173", "Endolysosomal dysfunction in radial glia progenitor cells leads to defective cerebral angiogenesis and compromised blood brain barrier integrity", "GSE270309", "Transcriptome Analysis", "The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to severe vascular defects hemorrhages and a leaky BBB. Altogether our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to severe vascular defects hemorrhages and a leaky BBB. Altogether our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to severe vascular defects hemorrhages and a leaky BBB. Altogether our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. Overall design: 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension . Sorting and RNA extraction was performed on TgBACscar2ba:KalTA4; UAS mKate2", null, "pubmed:39289367", null, "head wt rep 4", "GSM8339366", null, "source name:head|tissue:head|cell type:scarb2a+ cells|genotype:wt|geo loc name:missing|collection date:missing", "head wt rep 4", "done using the User friendly Transcriptomic Analysis Pipeline Assembly: danRer11 Supplementary files format and content: countsMatrix normalized.txt: expression dataset txt file contaning normalized UMI counts table for all samples.", "head", null, "For each experimental condition a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche trypsin B BI and DNAseI Roche the cell suspension was strained through a 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation RT and PCR. The final library concentration was measured by Qubit TapeStation and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing and each sample was sequenced for 6M reads.", null, "tissue:head|cell type:scarb2a+ cells|genotype:wt", "GSM8339366", "GSM8339366: head wt rep 4; Danio rerio; RNA Seq", "GSM8339366 r1", "GSM8339366", "1", "For each experimental condition a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche trypsin B BI and DNAseI Roche the cell suspension was strained through a 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation RT and PCR. The final library concentration was measured by Qubit TapeStation and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing and each sample was sequenced for 6M reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP515053", null, null, "scarb2_wt4_R1.fastq.gz scarb2_wt4_R2.fastq.gz", "fastq fastq", 723943430.0, 8722210.0, "GSM8339366 r1", "0:75 1:8", "A:206155698;C:145344454;G:172171717;T:200262536;N:9025", 75, 8, null, null, 206155698, 145344454, 172171717, 200262536, 9025, "SRX24989902", "SRS21691705", "SRA1904886", "Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science", "Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science", 2, 0.86958, 0.0, 0.0737, 0.0, 0.79928, 1.0, 0.47906, null, 75, 8, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2024-06-20", "Hatching", "Embryo", "Head", "Nervous System"], [32810, "SRR29478756", "SRX24989901", "SRS21691704", "SRP515053", "PRJNA1126173", "Endolysosomal dysfunction in radial glia progenitor cells leads to defective cerebral angiogenesis and compromised blood brain barrier integrity", "GSE270309", "Transcriptome Analysis", "The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to severe vascular defects hemorrhages and a leaky BBB. Altogether our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to severe vascular defects hemorrhages and a leaky BBB. Altogether our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to severe vascular defects hemorrhages and a leaky BBB. Altogether our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. Overall design: 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension . Sorting and RNA extraction was performed on TgBACscar2ba:KalTA4; UAS mKate2", null, "pubmed:39289367", null, "head wt rep 3", "GSM8339365", null, "source name:head|tissue:head|cell type:scarb2a+ cells|genotype:wt|geo loc name:missing|collection date:missing", "head wt rep 3", "done using the User friendly Transcriptomic Analysis Pipeline Assembly: danRer11 Supplementary files format and content: countsMatrix normalized.txt: expression dataset txt file contaning normalized UMI counts table for all samples.", "head", null, "For each experimental condition a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche trypsin B BI and DNAseI Roche the cell suspension was strained through a 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation RT and PCR. The final library concentration was measured by Qubit TapeStation and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing and each sample was sequenced for 6M reads.", null, "tissue:head|cell type:scarb2a+ cells|genotype:wt", "GSM8339365", "GSM8339365: head wt rep 3; Danio rerio; RNA Seq", "GSM8339365 r1", "GSM8339365", "1", "For each experimental condition a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche trypsin B BI and DNAseI Roche the cell suspension was strained through a 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation RT and PCR. The final library concentration was measured by Qubit TapeStation and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing and each sample was sequenced for 6M reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP515053", null, null, "scarb2_wt3_R1.fastq.gz scarb2_wt3_R2.fastq.gz", "fastq fastq", 560881132.0, 6757604.0, "GSM8339365 r1", "0:75 1:8", "A:158992539;C:112696361;G:133852695;T:155332822;N:6715", 75, 8, null, null, 158992539, 112696361, 133852695, 155332822, 6715, "SRX24989901", "SRS21691704", "SRA1904886", "Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science", "Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science", 2, 0.8706, 0.0, 0.07425, 0.0, 0.80038, 1.0, 0.47161, null, 75, 8, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2024-06-20", "Hatching", "Embryo", "Head", "Nervous System"], [32811, "SRR29478757", "SRX24989900", "SRS21691703", "SRP515053", "PRJNA1126173", "Endolysosomal dysfunction in radial glia progenitor cells leads to defective cerebral angiogenesis and compromised blood brain barrier integrity", "GSE270309", "Transcriptome Analysis", "The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to severe vascular defects hemorrhages and a leaky BBB. Altogether our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to severe vascular defects hemorrhages and a leaky BBB. Altogether our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity. While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration the underlying molecular mechanisms remain unclear. Here we use zebrafish embryos carrying a mutation in Scavenger Receptor B2 a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs to investigate the interplay among different NVU components. Through live imaging and genetic manipulations we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling leading to severe vascular defects hemorrhages and a leaky BBB. Altogether our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. Overall design: 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension . Sorting and RNA extraction was performed on TgBACscar2ba:KalTA4; UAS mKate2", null, "pubmed:39289367", null, "head wt rep 1", "GSM8339364", null, "source name:head|tissue:head|cell type:scarb2a+ cells|genotype:wt|geo loc name:missing|collection date:missing", "head wt rep 1", "done using the User friendly Transcriptomic Analysis Pipeline Assembly: danRer11 Supplementary files format and content: countsMatrix normalized.txt: expression dataset txt file contaning normalized UMI counts table for all samples.", "head", null, "For each experimental condition a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche trypsin B BI and DNAseI Roche the cell suspension was strained through a 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation RT and PCR. The final library concentration was measured by Qubit TapeStation and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing and each sample was sequenced for 6M reads.", null, "tissue:head|cell type:scarb2a+ cells|genotype:wt", "GSM8339364", "GSM8339364: head wt rep 1; Danio rerio; RNA Seq", "GSM8339364 r1", "GSM8339364", "1", "For each experimental condition a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche trypsin B BI and DNAseI Roche the cell suspension was strained through a 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation RT and PCR. The final library concentration was measured by Qubit TapeStation and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing and each sample was sequenced for 6M reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP515053", null, null, "scarb2_wt1_R1.fastq.gz scarb2_wt1_R2.fastq.gz", "fastq fastq", 539653799.0, 6501853.0, "GSM8339364 r1", "0:75 1:8", "A:153571518;C:110489477;G:128477853;T:147108152;N:6799", 75, 8, null, null, 153571518, 110489477, 128477853, 147108152, 6799, "SRX24989900", "SRS21691703", "SRA1904886", "Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science", "Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science", 2, 0.87359, 0.0, 0.07353, 0.0, 0.80184, 1.0, 0.47111, null, 75, 8, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2024-06-20", "Hatching", "Embryo", "Head", "Nervous System"], [53255, "SRR9825000", "SRX6581675", "SRS5147373", "SRP216247", "PRJNA556201", "Cross species analysis across 450 million yrs of evolution reveals conservation and divergence of the microglia program bulk RNA seq", "GSE134706", "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. The raw data for human subjects will be submitted through EGA for controlled access.", "parent bioproject:PRJNA556197", "pubmed:31835035", null, "MP 15 fish 3A.M", "GSM3963911", null, "source name:Total brain|strain:WT|tissue:Brain|selection markers:Ib4+|source:Thermo Fisher|age:4 5mo", "MP 15 fish 3A.M", "Illumina bcl2fastq software used for basecalling. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8 alignment: hisat 0.1.5 with deafult parameters filter PCR amplification bias using alignment break site and UMI barcode size 8. Read count by homer http://homer.salk.edu/homer/ngs/ 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: text files include mRNA molecule count values for each Sample", "Total brain", null, "10 000 cells from each sample were sorted into lysis/binding buffer Life Technologies. mRNA was captured with 6.5ul of Dynabeads oligodT Life Technologies washed and eluted at 85C with 10ul of 10 mM Tris HCl pH7.5. We used a derivation of the MARS seq as described Jaitin et al. Science 2014 developed for single cell MARS seq to produce three prime exprssion libraries with a minimum of 3 replicates per sample.", null, "strain:WT|tissue:Brain|selection markers:Ib4+|source:Thermo Fisher|catalog #:I32450|age:4 5mo", "GSM3963911", "GSM3963911: MP 15 fish 3A.M; Danio rerio; RNA Seq", "GSM3963911", null, "1", "10 000 cells from each sample were sorted into lysis/binding buffer Life Technologies. mRNA was captured with 6.5ul of Dynabeads oligodT Life Technologies washed and eluted at 85C with 10ul of 10 mM Tris HCl pH7.5. We used a derivation of the MARS seq as described Jaitin et al. Science 2014 developed for single cell MARS seq to produce three prime exprssion libraries with a minimum of 3 replicates per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP216247", null, "loader:fastq load.py|options: appendBCtoName", "MP_15_fish_3A.M.fastq.gz", "fastq", 438550950.0, 5847346.0, "GSM3963911 r1", "0:75", "A:133219954;C:87024588;G:96110755;T:122193517;N:2136", 75, null, null, null, 133219954, 87024588, 96110755, 122193517, 2136, "SRX6581675", "SRS5147373", "SRA926015", "GEO", "Immunology, Weizmann Institute of Science", 1, 0.85665, null, 0.14851, null, 0.83855, null, 0.48702, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2019-07-23", "Undetermined", "Undetermined", "Brain", "Nervous System"], [53256, "SRR9824999", "SRX6581674", "SRS5147372", "SRP216247", "PRJNA556201", "Cross species analysis across 450 million yrs of evolution reveals conservation and divergence of the microglia program bulk RNA seq", "GSE134706", "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. The raw data for human subjects will be submitted through EGA for controlled access.", "parent bioproject:PRJNA556197", "pubmed:31835035", null, "MP 14 fish 2A.M", "GSM3963910", null, "source name:Total brain|strain:WT|tissue:Brain|selection markers:Ib4+|source:Thermo Fisher|age:4 5mo", "MP 14 fish 2A.M", "Illumina bcl2fastq software used for basecalling. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8 alignment: hisat 0.1.5 with deafult parameters filter PCR amplification bias using alignment break site and UMI barcode size 8. Read count by homer http://homer.salk.edu/homer/ngs/ 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: text files include mRNA molecule count values for each Sample", "Total brain", null, "10 000 cells from each sample were sorted into lysis/binding buffer Life Technologies. mRNA was captured with 6.5ul of Dynabeads oligodT Life Technologies washed and eluted at 85C with 10ul of 10 mM Tris HCl pH7.5. We used a derivation of the MARS seq as described Jaitin et al. Science 2014 developed for single cell MARS seq to produce three prime exprssion libraries with a minimum of 3 replicates per sample.", null, "strain:WT|tissue:Brain|selection markers:Ib4+|source:Thermo Fisher|catalog #:I32450|age:4 5mo", "GSM3963910", "GSM3963910: MP 14 fish 2A.M; Danio rerio; RNA Seq", "GSM3963910", null, "1", "10 000 cells from each sample were sorted into lysis/binding buffer Life Technologies. mRNA was captured with 6.5ul of Dynabeads oligodT Life Technologies washed and eluted at 85C with 10ul of 10 mM Tris HCl pH7.5. We used a derivation of the MARS seq as described Jaitin et al. Science 2014 developed for single cell MARS seq to produce three prime exprssion libraries with a minimum of 3 replicates per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP216247", null, "loader:fastq load.py|options: appendBCtoName", "MP_14_fish_2A.M.fastq.gz", "fastq", 581871000.0, 7758280.0, "GSM3963910 r1", "0:75", "A:177443331;C:113767797;G:126832616;T:163824391;N:2865", 75, null, null, null, 177443331, 113767797, 126832616, 163824391, 2865, "SRX6581674", "SRS5147372", "SRA926015", "GEO", "Immunology, Weizmann Institute of Science", 1, 0.8556, null, 0.15773, null, 0.8356, null, 0.47849, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2019-07-23", "Undetermined", "Undetermined", "Brain", "Nervous System"], [53257, "SRR9824998", "SRX6581673", "SRS5147371", "SRP216247", "PRJNA556201", "Cross species analysis across 450 million yrs of evolution reveals conservation and divergence of the microglia program bulk RNA seq", "GSE134706", "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. The raw data for human subjects will be submitted through EGA for controlled access.", "parent bioproject:PRJNA556197", "pubmed:31835035", null, "MP 13 fish 1A.M", "GSM3963909", null, "source name:Total brain|strain:WT|tissue:Brain|selection markers:Ib4+|source:Thermo Fisher|age:4 5mo", "MP 13 fish 1A.M", "Illumina bcl2fastq software used for basecalling. Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8 alignment: hisat 0.1.5 with deafult parameters filter PCR amplification bias using alignment break site and UMI barcode size 8. Read count by homer http://homer.salk.edu/homer/ngs/ 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: text files include mRNA molecule count values for each Sample", "Total brain", null, "10 000 cells from each sample were sorted into lysis/binding buffer Life Technologies. mRNA was captured with 6.5ul of Dynabeads oligodT Life Technologies washed and eluted at 85C with 10ul of 10 mM Tris HCl pH7.5. We used a derivation of the MARS seq as described Jaitin et al. Science 2014 developed for single cell MARS seq to produce three prime exprssion libraries with a minimum of 3 replicates per sample.", null, "strain:WT|tissue:Brain|selection markers:Ib4+|source:Thermo Fisher|catalog #:I32450|age:4 5mo", "GSM3963909", "GSM3963909: MP 13 fish 1A.M; Danio rerio; RNA Seq", "GSM3963909", null, "1", "10 000 cells from each sample were sorted into lysis/binding buffer Life Technologies. mRNA was captured with 6.5ul of Dynabeads oligodT Life Technologies washed and eluted at 85C with 10ul of 10 mM Tris HCl pH7.5. We used a derivation of the MARS seq as described Jaitin et al. Science 2014 developed for single cell MARS seq to produce three prime exprssion libraries with a minimum of 3 replicates per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP216247", null, "loader:fastq load.py|options: appendBCtoName", "MP_13_fish_1A.M.fastq.gz", "fastq", 744772275.0, 9930297.0, "GSM3963909 r1", "0:75", "A:222652841;C:152631684;G:170650353;T:198833897;N:3500", 75, null, null, null, 222652841, 152631684, 170650353, 198833897, 3500, "SRX6581673", "SRS5147371", "SRA926015", "GEO", "Immunology, Weizmann Institute of Science", 1, 0.87523, null, 0.10463, null, 0.84812, null, 0.5271, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2019-07-23", "Undetermined", "Undetermined", "Brain", "Nervous System"], [68656, "SRR18097957", "SRX14248907", "SRS12068875", "SRP360907", "PRJNA809307", "Generation of specialized blood vessels via lymphatic transdifferentiation", "GSE197161", "Transcriptome Analysis", "The lineage and developmental trajectory of a cell are key determinant s of cellular identity. In the vascular system endothelial cells ECs of blood and lymphatic vessels LVs differentiate and diversify to cater the different physiological demands of each organ . While LVs are known to originate from multiple origins lymphatic ECs LECs themselves are not known to generate other cell types . Here we u s e recurrent imaging and lineage tracing of ECs in zebrafish anal fins AF from early development through maturity to uncover an unexpected mechanism of specialized blood vessel formation through transdifferentiation of LECs . Moreover we demonstrate distinct functional implications for deriving AF vessels from either LECs or blood ECs uncovering a link between cell ontogeny and functionality. We further use scRNA seq to characterize the different cellular populations and transition states involved in the transdifferentiation process . Finally we show that akin to its normal development the vasculature is re derived from lymphatics during AF regeneration demonstr ating that LECs in adult fish retain both potency and plasticity for generating blood ECs . Overall our work highlights a new innate mechanism of blood vess el formation through LEC trans differentiation and provides in vivo evidence for a link between cell ontogeny and functionality in ECs Overall design: 80 anal fins from immature zebrafish were digested. Sorting and RNA extraction was performed on fli1a:dsRed positive cells", null, "pubmed:35614218", null, "Immature fin ECs plate3", "GSM5910460", null, "source name:fli1a:dsRed positive cells|tissue:Anal fin|cell type:endothelial cells|Stage:II III", "Immature fin ECs plate3", "GRCz10 genome mapping was done using Bowtie2 with default parameters Demultiplexing and UMI count matrixes were based on 4bp pool barcodes in Read1 for each sample. 8bp of UMI with 7bp of cell barcodes in Read2 and performed as described in Jaitin et al. 2014 Genome build: GRCz10 Supplementary files format and content: AB006.txt AB007.txt AB008.txt: expression dataset txt files containing UMI counts table per plate. Single cell metadata p1.xslx: xslx file sheet1 pool barcode of plate1 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate1 analyzed cell names. Single cell metadata p2.xslx: xslx file sheet1 pool barcode of plate2 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate2 analyzed cell names. Single cell metadata p3.xslx: xslx file sheet1 pool barcode of plate3 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate3 analyzed cell names", "fli1a:dsRed positive cells", null, "80 anal fins were dissected manually chopped with a sterile razor and enzymatically digested using Liberase I Trypsin B and DNaseI. Single cells were sorted into 384 well plates containing lysis solution UPW 8nM poly dT barcodes 0.1%triton and RNAse inhibitor MARS seq libraries were prepared as described Jaitin et al Science 2014", null, "tissue:Anal fin|cell type:endothelial cells|Stage:II III", "GSM5910460", "GSM5910460: Immature fin ECs plate3; Danio rerio; RNA Seq", "GSM5910460 r1", "GSM5910460", "1", "80 anal fins were dissected manually chopped with a sterile razor and enzymatically digested using Liberase I Trypsin B and DNaseI. Single cells were sorted into 384 well plates containing lysis solution UPW 8nM poly dT barcodes 0.1%triton and RNAse inhibitor MARS seq libraries were prepared as described Jaitin et al Science 2014", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP360907", null, null, "BC3_S0_R1_001.fastq.gz BC3_S0_R2_001.fastq.gz", "fastq fastq", 5000226570.0, 55558073.0, "GSM5910460 r1", "0:75 1:15", "A:1398279779;C:1105834990;G:1278168650;T:1217071842;N:871309", 75, 15, null, null, 1398279779, 1105834990, 1278168650, 1217071842, 871309, "SRX14248907", "SRS12068875", "SRA1376737", "Weizmann Institute of Science", "Department of Biological Regulation, Weizmann Institute of Science", 2, 0.75587, 0.0, 0.22384, 0.0, 0.87665, 1.0, 0.59533, null, 75, 15, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2022-02-22", "Undetermined", "Adult", "Fin", "Surface Structure"], [68657, "SRR18097958", "SRX14248906", "SRS12068874", "SRP360907", "PRJNA809307", "Generation of specialized blood vessels via lymphatic transdifferentiation", "GSE197161", "Transcriptome Analysis", "The lineage and developmental trajectory of a cell are key determinant s of cellular identity. In the vascular system endothelial cells ECs of blood and lymphatic vessels LVs differentiate and diversify to cater the different physiological demands of each organ . While LVs are known to originate from multiple origins lymphatic ECs LECs themselves are not known to generate other cell types . Here we u s e recurrent imaging and lineage tracing of ECs in zebrafish anal fins AF from early development through maturity to uncover an unexpected mechanism of specialized blood vessel formation through transdifferentiation of LECs . Moreover we demonstrate distinct functional implications for deriving AF vessels from either LECs or blood ECs uncovering a link between cell ontogeny and functionality. We further use scRNA seq to characterize the different cellular populations and transition states involved in the transdifferentiation process . Finally we show that akin to its normal development the vasculature is re derived from lymphatics during AF regeneration demonstr ating that LECs in adult fish retain both potency and plasticity for generating blood ECs . Overall our work highlights a new innate mechanism of blood vess el formation through LEC trans differentiation and provides in vivo evidence for a link between cell ontogeny and functionality in ECs Overall design: 80 anal fins from immature zebrafish were digested. Sorting and RNA extraction was performed on fli1a:dsRed positive cells", null, "pubmed:35614218", null, "Immature fin ECs plate2", "GSM5910459", null, "source name:fli1a:dsRed positive cells|tissue:Anal fin|cell type:endothelial cells|Stage:II III", "Immature fin ECs plate2", "GRCz10 genome mapping was done using Bowtie2 with default parameters Demultiplexing and UMI count matrixes were based on 4bp pool barcodes in Read1 for each sample. 8bp of UMI with 7bp of cell barcodes in Read2 and performed as described in Jaitin et al. 2014 Genome build: GRCz10 Supplementary files format and content: AB006.txt AB007.txt AB008.txt: expression dataset txt files containing UMI counts table per plate. Single cell metadata p1.xslx: xslx file sheet1 pool barcode of plate1 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate1 analyzed cell names. Single cell metadata p2.xslx: xslx file sheet1 pool barcode of plate2 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate2 analyzed cell names. Single cell metadata p3.xslx: xslx file sheet1 pool barcode of plate3 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate3 analyzed cell names", "fli1a:dsRed positive cells", null, "80 anal fins were dissected manually chopped with a sterile razor and enzymatically digested using Liberase I Trypsin B and DNaseI. Single cells were sorted into 384 well plates containing lysis solution UPW 8nM poly dT barcodes 0.1%triton and RNAse inhibitor MARS seq libraries were prepared as described Jaitin et al Science 2014", null, "tissue:Anal fin|cell type:endothelial cells|Stage:II III", "GSM5910459", "GSM5910459: Immature fin ECs plate2; Danio rerio; RNA Seq", "GSM5910459 r1", "GSM5910459", "1", "80 anal fins were dissected manually chopped with a sterile razor and enzymatically digested using Liberase I Trypsin B and DNaseI. 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In the vascular system endothelial cells ECs of blood and lymphatic vessels LVs differentiate and diversify to cater the different physiological demands of each organ . While LVs are known to originate from multiple origins lymphatic ECs LECs themselves are not known to generate other cell types . Here we u s e recurrent imaging and lineage tracing of ECs in zebrafish anal fins AF from early development through maturity to uncover an unexpected mechanism of specialized blood vessel formation through transdifferentiation of LECs . Moreover we demonstrate distinct functional implications for deriving AF vessels from either LECs or blood ECs uncovering a link between cell ontogeny and functionality. We further use scRNA seq to characterize the different cellular populations and transition states involved in the transdifferentiation process . Finally we show that akin to its normal development the vasculature is re derived from lymphatics during AF regeneration demonstr ating that LECs in adult fish retain both potency and plasticity for generating blood ECs . Overall our work highlights a new innate mechanism of blood vess el formation through LEC trans differentiation and provides in vivo evidence for a link between cell ontogeny and functionality in ECs Overall design: 80 anal fins from immature zebrafish were digested. Sorting and RNA extraction was performed on fli1a:dsRed positive cells", null, "pubmed:35614218", null, "Immature fin ECs plate1", "GSM5910458", null, "source name:fli1a:dsRed positive cells|tissue:Anal fin|cell type:endothelial cells|Stage:II III", "Immature fin ECs plate1", "GRCz10 genome mapping was done using Bowtie2 with default parameters Demultiplexing and UMI count matrixes were based on 4bp pool barcodes in Read1 for each sample. 8bp of UMI with 7bp of cell barcodes in Read2 and performed as described in Jaitin et al. 2014 Genome build: GRCz10 Supplementary files format and content: AB006.txt AB007.txt AB008.txt: expression dataset txt files containing UMI counts table per plate. Single cell metadata p1.xslx: xslx file sheet1 pool barcode of plate1 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate1 analyzed cell names. Single cell metadata p2.xslx: xslx file sheet1 pool barcode of plate2 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate2 analyzed cell names. Single cell metadata p3.xslx: xslx file sheet1 pool barcode of plate3 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate3 analyzed cell names", "fli1a:dsRed positive cells", null, "80 anal fins were dissected manually chopped with a sterile razor and enzymatically digested using Liberase I Trypsin B and DNaseI. 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