metadata: run_metadata: 6 rows where devstage_curation = "Hatching" and technology = "marsseq"

6 rows where devstage_curation = "Hatching" and technology = "marsseq"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
32806	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 sever…	pubmed:39289367	head scarb2a mut rep 3	GSM8339369	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	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 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl 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 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ 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.	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 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl 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 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ 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.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP515053	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	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	0.06751	0.80081	1.0	0.47421	75	8	B	T	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	marsseq	Israel	2024-06-20	Hatching	Embryo	Head	Nervous System
32807	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 sever…	pubmed:39289367	head scarb2a mut rep 2	GSM8339368	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	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 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl 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 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ 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.	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 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl 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 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ 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.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP515053	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	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	0.06116	0.80438	1.0	0.47226	75	8	B	T	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	marsseq	Israel	2024-06-20	Hatching	Embryo	Head	Nervous System
32808	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 sever…	pubmed:39289367	head scarb2a mut rep 1	GSM8339367	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	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 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl 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 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ 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.	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 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl 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 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ 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.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP515053	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	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	0.06577	0.80359	1.0	0.48395	75	8	B	T	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	marsseq	Israel	2024-06-20	Hatching	Embryo	Head	Nervous System
32809	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 sever…	pubmed:39289367	head wt rep 4	GSM8339366	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	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 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl 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 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ 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.	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 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl 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 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ 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.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP515053	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	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	0.0737	0.79928	1.0	0.47906	75	8	B	T	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	marsseq	Israel	2024-06-20	Hatching	Embryo	Head	Nervous System
32810	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 sever…	pubmed:39289367	head wt rep 3	GSM8339365	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	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 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl 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 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ 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.	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 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl 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 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ 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.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP515053	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	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	0.07425	0.80038	1.0	0.47161	75	8	B	T	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	marsseq	Israel	2024-06-20	Hatching	Embryo	Head	Nervous System
32811	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 sever…	pubmed:39289367	head wt rep 1	GSM8339364	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	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 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl 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 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ 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.	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 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl 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 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ 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.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP515053	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	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	0.07353	0.80184	1.0	0.47111	75	8	B	T	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	marsseq	Israel	2024-06-20	Hatching	Embryo	Head	Nervous System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;