{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_strategy = \"RNA-Seq\", experiment.platform = \"ILLUMINA\" 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"], [36249, "SRR34017907", "SRX29213468", "SRS25409913", "SRP592701", "PRJNA1278741", "Single cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches [scRNA Seq]", "GSE300039", "Transcriptome Analysis", "Hematopoietic stem cells HSCs and more committed progenitors collectively referred to as HSPCs emerge from vessels during development  via Endothelial to Hematopoietic Transition EHT. Recently  using the zebrafish embryo  we showed that two EHT cell types emerge from the dorsal aorta  raising the question of their subsequent fate. To address this issue  we established a complex pipeline based on single cell photoconversion and transgenic lines to characterize the abilities of EHT cell progenies to conquer hematopoietic organs and to obtain their transcriptomic profiles. We show that the two EHT cell types lead to partly differentially fated cells  with significant differences in thymus colonization and T lymphoid lineage commitment. In addition  we investigated implantation of HSPCs in niches  with the support of HSPC signatures gata2b and cd34/podocalyxin  retrieved from our single cell datasets. This revealed  at unprecedented resolution  the homing of HSPCs in niches of entire early larvae  including the pronephros  the sub aortic and caudal regions  as well as the area contacting the supra intestinal artery. Our work provides new insights on fundamental aspects of HSPC fate acquisition  from their emergence to their homing in specific niches. Overall design: Single cell transcriptomics analysis of newly born hematopoietic stem and progenitor cells. This dataset comprises progenies of cells photoconverted at 2dpf and sorted by FACS at 5dpf  using the Tgkdrl:nls kikume transgenic line  as well as sorted FACS hematopoietic cells from transgenic reporter lines  namely from the Tgrunx1+23:eGFP and the outcross of the Tgcd41:eGFP and Tggata2b:RFP lines. Larvae were collected post dissection separating the rostral  anterior and posterior region along a transversal section at the posterior limit of the elongated yolk and at the posterior limit of the swim bladder  dissociation and sorting using a BD FACS AriaIII cell sorter. Progenies of photoconverted cells comprise progenies of single EHT photoconversion either EHT pol+ or EHT pol  or whole hemogenic endothelium photoconversion. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019.", null, "pubmed:40501392", null, "5 dpf hematopoietic zebrafish cells  session 2", "GSM9052756", null, "tissue:sorted hematopoietic cells|cell type:sorted hematopoietic cells|geo loc name:missing|collection date:missing", "5 dpf hematopoietic zebrafish cells  session 2", "Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019 Assembly: zebrafish genome Lawson lab version 4.3.2. Supplementary files format and content: Tab separated value files", "sorted hematopoietic cells", null, "Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al.  2018; Manoli and Driever  2012; Samsa et al.  2016. All steps were performed with cooled solutions 4\u00b0C  and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly  5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine  at a final concentration of 640 \u00b5g/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4\u00b0C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies  Cat#: 12605 010 for 10 min on ice  with gentle pipetting every 3 mins  first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g  before the TrypLE was removed and the cells were resuspended in 500 \u00b5l FACSmax medium Genlantis  Cat#: T200100. Ultimately  samples were passed through a 40 \u03bcm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 \u00b5l of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples  gating was done on SSC A vs. FSC A to collect cells  then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher  Cat#: D15106. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019. Briefly  a first step of reverse transcription RT SuperScript III  Thermo Fisher  Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT  primers were removed with an exonuclease ExoI NEB  Cat#: M0293L  and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit  NEB  Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit  NEB  Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher  Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher  Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase  Agilent  Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix  Roche Diagnostics  Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and \u00df actin  DNA quality control using a TapeStation  Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.", null, "cell type:sorted hematopoietic cells", "GSM9052756", "GSM9052756: 5 dpf hematopoietic zebrafish cells  session 2; Danio rerio; RNA Seq", "GSM9052756 r1", "GSM9052756", "1", "Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al.  2018; Manoli and Driever  2012; Samsa et al.  2016. All steps were performed with cooled solutions 4\u00b0C  and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly  5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine  at a final concentration of 640 \u00b5g/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4\u00b0C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies  Cat#: 12605 010 for 10 min on ice  with gentle pipetting every 3 mins  first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g  before the TrypLE was removed and the cells were resuspended in 500 \u00b5l FACSmax medium Genlantis  Cat#: T200100. Ultimately  samples were passed through a 40 \u03bcm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 \u00b5l of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples  gating was done on SSC A vs. FSC A to collect cells  then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher  Cat#: D15106. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019. Briefly  a first step of reverse transcription RT SuperScript III  Thermo Fisher  Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT  primers were removed with an exonuclease ExoI NEB  Cat#: M0293L  and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit  NEB  Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit  NEB  Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher  Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher  Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase  Agilent  Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix  Roche Diagnostics  Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and \u00df actin  DNA quality control using a TapeStation  Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP592701", null, null, "TORCQ_2023_S0_L001_R1_001.fastq.gz TORCQ_2023_S0_L001_R2_001.fastq.gz", "fastq fastq", 9123251137.0, 118483781.0, "GSM9052756 r1", "0:57 1:20", "A:2003237489;C:1403878506;G:1540717140;T:1805684398;N:2369733604", 57, 20, null, null, 2003237489, 1403878506, 1540717140, 1805684398, 2369733604, "SRX29213468", "SRS25409913", "SRA2151098", "Institut Pasteur", "Institut Pasteur", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "marsseq", null, "France", "2025-06-17", "Larval", "Larval", "Blood", "Hematopoietic System"], [36250, "SRR34017908", "SRX29213468", "SRS25409913", "SRP592701", "PRJNA1278741", "Single cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches [scRNA Seq]", "GSE300039", "Transcriptome Analysis", "Hematopoietic stem cells HSCs and more committed progenitors collectively referred to as HSPCs emerge from vessels during development  via Endothelial to Hematopoietic Transition EHT. Recently  using the zebrafish embryo  we showed that two EHT cell types emerge from the dorsal aorta  raising the question of their subsequent fate. To address this issue  we established a complex pipeline based on single cell photoconversion and transgenic lines to characterize the abilities of EHT cell progenies to conquer hematopoietic organs and to obtain their transcriptomic profiles. We show that the two EHT cell types lead to partly differentially fated cells  with significant differences in thymus colonization and T lymphoid lineage commitment. In addition  we investigated implantation of HSPCs in niches  with the support of HSPC signatures gata2b and cd34/podocalyxin  retrieved from our single cell datasets. This revealed  at unprecedented resolution  the homing of HSPCs in niches of entire early larvae  including the pronephros  the sub aortic and caudal regions  as well as the area contacting the supra intestinal artery. Our work provides new insights on fundamental aspects of HSPC fate acquisition  from their emergence to their homing in specific niches. Overall design: Single cell transcriptomics analysis of newly born hematopoietic stem and progenitor cells. This dataset comprises progenies of cells photoconverted at 2dpf and sorted by FACS at 5dpf  using the Tgkdrl:nls kikume transgenic line  as well as sorted FACS hematopoietic cells from transgenic reporter lines  namely from the Tgrunx1+23:eGFP and the outcross of the Tgcd41:eGFP and Tggata2b:RFP lines. Larvae were collected post dissection separating the rostral  anterior and posterior region along a transversal section at the posterior limit of the elongated yolk and at the posterior limit of the swim bladder  dissociation and sorting using a BD FACS AriaIII cell sorter. Progenies of photoconverted cells comprise progenies of single EHT photoconversion either EHT pol+ or EHT pol  or whole hemogenic endothelium photoconversion. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019.", null, "pubmed:40501392", null, "5 dpf hematopoietic zebrafish cells  session 2", "GSM9052756", null, "tissue:sorted hematopoietic cells|cell type:sorted hematopoietic cells|geo loc name:missing|collection date:missing", "5 dpf hematopoietic zebrafish cells  session 2", "Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019 Assembly: zebrafish genome Lawson lab version 4.3.2. Supplementary files format and content: Tab separated value files", "sorted hematopoietic cells", null, "Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al.  2018; Manoli and Driever  2012; Samsa et al.  2016. All steps were performed with cooled solutions 4\u00b0C  and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly  5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine  at a final concentration of 640 \u00b5g/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4\u00b0C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies  Cat#: 12605 010 for 10 min on ice  with gentle pipetting every 3 mins  first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g  before the TrypLE was removed and the cells were resuspended in 500 \u00b5l FACSmax medium Genlantis  Cat#: T200100. Ultimately  samples were passed through a 40 \u03bcm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 \u00b5l of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples  gating was done on SSC A vs. FSC A to collect cells  then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher  Cat#: D15106. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019. Briefly  a first step of reverse transcription RT SuperScript III  Thermo Fisher  Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT  primers were removed with an exonuclease ExoI NEB  Cat#: M0293L  and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit  NEB  Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit  NEB  Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher  Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher  Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase  Agilent  Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix  Roche Diagnostics  Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and \u00df actin  DNA quality control using a TapeStation  Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.", null, "cell type:sorted hematopoietic cells", "GSM9052756", "GSM9052756: 5 dpf hematopoietic zebrafish cells  session 2; Danio rerio; RNA Seq", "GSM9052756 r1", "GSM9052756", "1", "Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al.  2018; Manoli and Driever  2012; Samsa et al.  2016. All steps were performed with cooled solutions 4\u00b0C  and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly  5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine  at a final concentration of 640 \u00b5g/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4\u00b0C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies  Cat#: 12605 010 for 10 min on ice  with gentle pipetting every 3 mins  first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g  before the TrypLE was removed and the cells were resuspended in 500 \u00b5l FACSmax medium Genlantis  Cat#: T200100. Ultimately  samples were passed through a 40 \u03bcm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 \u00b5l of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples  gating was done on SSC A vs. FSC A to collect cells  then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher  Cat#: D15106. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019. Briefly  a first step of reverse transcription RT SuperScript III  Thermo Fisher  Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT  primers were removed with an exonuclease ExoI NEB  Cat#: M0293L  and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit  NEB  Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit  NEB  Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher  Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher  Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase  Agilent  Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix  Roche Diagnostics  Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and \u00df actin  DNA quality control using a TapeStation  Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP592701", null, null, "TORCQ_2023_S0_L002_R1_001.fastq.gz TORCQ_2023_S0_L002_R2_001.fastq.gz", "fastq fastq", 9249291128.0, 120120664.0, "GSM9052756 r2", "0:57 1:20", "A:2023532922;C:1427491871;G:1568162363;T:1827659977;N:2402443995", 57, 20, null, null, 2023532922, 1427491871, 1568162363, 1827659977, 2402443995, "SRX29213468", "SRS25409913", "SRA2151098", "Institut Pasteur", "Institut Pasteur", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "marsseq", null, "France", "2025-06-17", "Larval", "Larval", "Blood", "Hematopoietic System"], [36251, "SRR34017909", "SRX29213468", "SRS25409913", "SRP592701", "PRJNA1278741", "Single cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches [scRNA Seq]", "GSE300039", "Transcriptome Analysis", "Hematopoietic stem cells HSCs and more committed progenitors collectively referred to as HSPCs emerge from vessels during development  via Endothelial to Hematopoietic Transition EHT. Recently  using the zebrafish embryo  we showed that two EHT cell types emerge from the dorsal aorta  raising the question of their subsequent fate. To address this issue  we established a complex pipeline based on single cell photoconversion and transgenic lines to characterize the abilities of EHT cell progenies to conquer hematopoietic organs and to obtain their transcriptomic profiles. We show that the two EHT cell types lead to partly differentially fated cells  with significant differences in thymus colonization and T lymphoid lineage commitment. In addition  we investigated implantation of HSPCs in niches  with the support of HSPC signatures gata2b and cd34/podocalyxin  retrieved from our single cell datasets. This revealed  at unprecedented resolution  the homing of HSPCs in niches of entire early larvae  including the pronephros  the sub aortic and caudal regions  as well as the area contacting the supra intestinal artery. Our work provides new insights on fundamental aspects of HSPC fate acquisition  from their emergence to their homing in specific niches. Overall design: Single cell transcriptomics analysis of newly born hematopoietic stem and progenitor cells. This dataset comprises progenies of cells photoconverted at 2dpf and sorted by FACS at 5dpf  using the Tgkdrl:nls kikume transgenic line  as well as sorted FACS hematopoietic cells from transgenic reporter lines  namely from the Tgrunx1+23:eGFP and the outcross of the Tgcd41:eGFP and Tggata2b:RFP lines. Larvae were collected post dissection separating the rostral  anterior and posterior region along a transversal section at the posterior limit of the elongated yolk and at the posterior limit of the swim bladder  dissociation and sorting using a BD FACS AriaIII cell sorter. Progenies of photoconverted cells comprise progenies of single EHT photoconversion either EHT pol+ or EHT pol  or whole hemogenic endothelium photoconversion. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019.", null, "pubmed:40501392", null, "5 dpf hematopoietic zebrafish cells  session 2", "GSM9052756", null, "tissue:sorted hematopoietic cells|cell type:sorted hematopoietic cells|geo loc name:missing|collection date:missing", "5 dpf hematopoietic zebrafish cells  session 2", "Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019 Assembly: zebrafish genome Lawson lab version 4.3.2. Supplementary files format and content: Tab separated value files", "sorted hematopoietic cells", null, "Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al.  2018; Manoli and Driever  2012; Samsa et al.  2016. All steps were performed with cooled solutions 4\u00b0C  and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly  5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine  at a final concentration of 640 \u00b5g/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4\u00b0C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies  Cat#: 12605 010 for 10 min on ice  with gentle pipetting every 3 mins  first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g  before the TrypLE was removed and the cells were resuspended in 500 \u00b5l FACSmax medium Genlantis  Cat#: T200100. Ultimately  samples were passed through a 40 \u03bcm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 \u00b5l of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples  gating was done on SSC A vs. FSC A to collect cells  then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher  Cat#: D15106. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019. Briefly  a first step of reverse transcription RT SuperScript III  Thermo Fisher  Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT  primers were removed with an exonuclease ExoI NEB  Cat#: M0293L  and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit  NEB  Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit  NEB  Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher  Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher  Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase  Agilent  Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix  Roche Diagnostics  Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and \u00df actin  DNA quality control using a TapeStation  Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.", null, "cell type:sorted hematopoietic cells", "GSM9052756", "GSM9052756: 5 dpf hematopoietic zebrafish cells  session 2; Danio rerio; RNA Seq", "GSM9052756 r1", "GSM9052756", "1", "Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al.  2018; Manoli and Driever  2012; Samsa et al.  2016. All steps were performed with cooled solutions 4\u00b0C  and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly  5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine  at a final concentration of 640 \u00b5g/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4\u00b0C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies  Cat#: 12605 010 for 10 min on ice  with gentle pipetting every 3 mins  first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g  before the TrypLE was removed and the cells were resuspended in 500 \u00b5l FACSmax medium Genlantis  Cat#: T200100. Ultimately  samples were passed through a 40 \u03bcm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 \u00b5l of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples  gating was done on SSC A vs. FSC A to collect cells  then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher  Cat#: D15106. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019. Briefly  a first step of reverse transcription RT SuperScript III  Thermo Fisher  Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT  primers were removed with an exonuclease ExoI NEB  Cat#: M0293L  and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit  NEB  Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit  NEB  Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher  Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher  Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase  Agilent  Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix  Roche Diagnostics  Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and \u00df actin  DNA quality control using a TapeStation  Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP592701", null, null, "TORCQ_2023_S0_L003_R1_001.fastq.gz TORCQ_2023_S0_L003_R2_001.fastq.gz", "fastq fastq", 9438695574.0, 122580462.0, "GSM9052756 r3", "0:57 1:20", "A:2061159862;C:1455510691;G:1599304279;T:1871072315;N:2451648427", 57, 20, null, null, 2061159862, 1455510691, 1599304279, 1871072315, 2451648427, "SRX29213468", "SRS25409913", "SRA2151098", "Institut Pasteur", "Institut Pasteur", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "marsseq", null, "France", "2025-06-17", "Larval", "Larval", "Blood", "Hematopoietic System"], [36252, "SRR34017910", "SRX29213468", "SRS25409913", "SRP592701", "PRJNA1278741", "Single cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches [scRNA Seq]", "GSE300039", "Transcriptome Analysis", "Hematopoietic stem cells HSCs and more committed progenitors collectively referred to as HSPCs emerge from vessels during development  via Endothelial to Hematopoietic Transition EHT. Recently  using the zebrafish embryo  we showed that two EHT cell types emerge from the dorsal aorta  raising the question of their subsequent fate. To address this issue  we established a complex pipeline based on single cell photoconversion and transgenic lines to characterize the abilities of EHT cell progenies to conquer hematopoietic organs and to obtain their transcriptomic profiles. We show that the two EHT cell types lead to partly differentially fated cells  with significant differences in thymus colonization and T lymphoid lineage commitment. In addition  we investigated implantation of HSPCs in niches  with the support of HSPC signatures gata2b and cd34/podocalyxin  retrieved from our single cell datasets. This revealed  at unprecedented resolution  the homing of HSPCs in niches of entire early larvae  including the pronephros  the sub aortic and caudal regions  as well as the area contacting the supra intestinal artery. Our work provides new insights on fundamental aspects of HSPC fate acquisition  from their emergence to their homing in specific niches. Overall design: Single cell transcriptomics analysis of newly born hematopoietic stem and progenitor cells. This dataset comprises progenies of cells photoconverted at 2dpf and sorted by FACS at 5dpf  using the Tgkdrl:nls kikume transgenic line  as well as sorted FACS hematopoietic cells from transgenic reporter lines  namely from the Tgrunx1+23:eGFP and the outcross of the Tgcd41:eGFP and Tggata2b:RFP lines. Larvae were collected post dissection separating the rostral  anterior and posterior region along a transversal section at the posterior limit of the elongated yolk and at the posterior limit of the swim bladder  dissociation and sorting using a BD FACS AriaIII cell sorter. Progenies of photoconverted cells comprise progenies of single EHT photoconversion either EHT pol+ or EHT pol  or whole hemogenic endothelium photoconversion. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019.", null, "pubmed:40501392", null, "5 dpf hematopoietic zebrafish cells  session 2", "GSM9052756", null, "tissue:sorted hematopoietic cells|cell type:sorted hematopoietic cells|geo loc name:missing|collection date:missing", "5 dpf hematopoietic zebrafish cells  session 2", "Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019 Assembly: zebrafish genome Lawson lab version 4.3.2. Supplementary files format and content: Tab separated value files", "sorted hematopoietic cells", null, "Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al.  2018; Manoli and Driever  2012; Samsa et al.  2016. All steps were performed with cooled solutions 4\u00b0C  and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly  5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine  at a final concentration of 640 \u00b5g/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4\u00b0C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies  Cat#: 12605 010 for 10 min on ice  with gentle pipetting every 3 mins  first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g  before the TrypLE was removed and the cells were resuspended in 500 \u00b5l FACSmax medium Genlantis  Cat#: T200100. Ultimately  samples were passed through a 40 \u03bcm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 \u00b5l of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples  gating was done on SSC A vs. FSC A to collect cells  then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher  Cat#: D15106. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019. Briefly  a first step of reverse transcription RT SuperScript III  Thermo Fisher  Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT  primers were removed with an exonuclease ExoI NEB  Cat#: M0293L  and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit  NEB  Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit  NEB  Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher  Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher  Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase  Agilent  Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix  Roche Diagnostics  Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and \u00df actin  DNA quality control using a TapeStation  Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.", null, "cell type:sorted hematopoietic cells", "GSM9052756", "GSM9052756: 5 dpf hematopoietic zebrafish cells  session 2; Danio rerio; RNA Seq", "GSM9052756 r1", "GSM9052756", "1", "Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al.  2018; Manoli and Driever  2012; Samsa et al.  2016. All steps were performed with cooled solutions 4\u00b0C  and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly  5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine  at a final concentration of 640 \u00b5g/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4\u00b0C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies  Cat#: 12605 010 for 10 min on ice  with gentle pipetting every 3 mins  first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g  before the TrypLE was removed and the cells were resuspended in 500 \u00b5l FACSmax medium Genlantis  Cat#: T200100. Ultimately  samples were passed through a 40 \u03bcm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 \u00b5l of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples  gating was done on SSC A vs. FSC A to collect cells  then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher  Cat#: D15106. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019. Briefly  a first step of reverse transcription RT SuperScript III  Thermo Fisher  Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT  primers were removed with an exonuclease ExoI NEB  Cat#: M0293L  and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit  NEB  Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit  NEB  Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher  Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher  Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase  Agilent  Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix  Roche Diagnostics  Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and \u00df actin  DNA quality control using a TapeStation  Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP592701", null, null, "TORCQ_2023_S0_L004_R1_001.fastq.gz TORCQ_2023_S0_L004_R2_001.fastq.gz", "fastq fastq", 9409346870.0, 122199310.0, "GSM9052756 r4", "0:57 1:20", "A:2048111796;C:1451606983;G:1595602008;T:1870010070;N:2444016013", 57, 20, null, null, 2048111796, 1451606983, 1595602008, 1870010070, 2444016013, "SRX29213468", "SRS25409913", "SRA2151098", "Institut Pasteur", "Institut Pasteur", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "marsseq", null, "France", "2025-06-17", "Larval", "Larval", "Blood", "Hematopoietic System"], [36253, "SRR34017905", "SRX29213467", "SRS25409912", "SRP592701", "PRJNA1278741", "Single cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches [scRNA Seq]", "GSE300039", "Transcriptome Analysis", "Hematopoietic stem cells HSCs and more committed progenitors collectively referred to as HSPCs emerge from vessels during development  via Endothelial to Hematopoietic Transition EHT. Recently  using the zebrafish embryo  we showed that two EHT cell types emerge from the dorsal aorta  raising the question of their subsequent fate. To address this issue  we established a complex pipeline based on single cell photoconversion and transgenic lines to characterize the abilities of EHT cell progenies to conquer hematopoietic organs and to obtain their transcriptomic profiles. We show that the two EHT cell types lead to partly differentially fated cells  with significant differences in thymus colonization and T lymphoid lineage commitment. In addition  we investigated implantation of HSPCs in niches  with the support of HSPC signatures gata2b and cd34/podocalyxin  retrieved from our single cell datasets. This revealed  at unprecedented resolution  the homing of HSPCs in niches of entire early larvae  including the pronephros  the sub aortic and caudal regions  as well as the area contacting the supra intestinal artery. Our work provides new insights on fundamental aspects of HSPC fate acquisition  from their emergence to their homing in specific niches. Overall design: Single cell transcriptomics analysis of newly born hematopoietic stem and progenitor cells. This dataset comprises progenies of cells photoconverted at 2dpf and sorted by FACS at 5dpf  using the Tgkdrl:nls kikume transgenic line  as well as sorted FACS hematopoietic cells from transgenic reporter lines  namely from the Tgrunx1+23:eGFP and the outcross of the Tgcd41:eGFP and Tggata2b:RFP lines. Larvae were collected post dissection separating the rostral  anterior and posterior region along a transversal section at the posterior limit of the elongated yolk and at the posterior limit of the swim bladder  dissociation and sorting using a BD FACS AriaIII cell sorter. Progenies of photoconverted cells comprise progenies of single EHT photoconversion either EHT pol+ or EHT pol  or whole hemogenic endothelium photoconversion. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019.", null, "pubmed:40501392", null, "5 dpf hematopoietic zebrafish cells  session 1", "GSM9052755", null, "tissue:sorted hematopoietic cells|cell type:sorted hematopoietic cells|geo loc name:missing|collection date:missing", "5 dpf hematopoietic zebrafish cells  session 1", "Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019 Assembly: zebrafish genome Lawson lab version 4.3.2. Supplementary files format and content: Tab separated value files", "sorted hematopoietic cells", null, "Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al.  2018; Manoli and Driever  2012; Samsa et al.  2016. All steps were performed with cooled solutions 4\u00b0C  and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly  5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine  at a final concentration of 640 \u00b5g/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4\u00b0C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies  Cat#: 12605 010 for 10 min on ice  with gentle pipetting every 3 mins  first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g  before the TrypLE was removed and the cells were resuspended in 500 \u00b5l FACSmax medium Genlantis  Cat#: T200100. Ultimately  samples were passed through a 40 \u03bcm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 \u00b5l of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples  gating was done on SSC A vs. FSC A to collect cells  then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher  Cat#: D15106. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019. Briefly  a first step of reverse transcription RT SuperScript III  Thermo Fisher  Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT  primers were removed with an exonuclease ExoI NEB  Cat#: M0293L  and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit  NEB  Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit  NEB  Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher  Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher  Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase  Agilent  Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix  Roche Diagnostics  Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and \u00df actin  DNA quality control using a TapeStation  Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.", null, "cell type:sorted hematopoietic cells", "GSM9052755", "GSM9052755: 5 dpf hematopoietic zebrafish cells  session 1; Danio rerio; RNA Seq", "GSM9052755 r1", "GSM9052755", "1", "Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al.  2018; Manoli and Driever  2012; Samsa et al.  2016. All steps were performed with cooled solutions 4\u00b0C  and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly  5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine  at a final concentration of 640 \u00b5g/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4\u00b0C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies  Cat#: 12605 010 for 10 min on ice  with gentle pipetting every 3 mins  first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g  before the TrypLE was removed and the cells were resuspended in 500 \u00b5l FACSmax medium Genlantis  Cat#: T200100. Ultimately  samples were passed through a 40 \u03bcm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 \u00b5l of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples  gating was done on SSC A vs. FSC A to collect cells  then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher  Cat#: D15106. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019. Briefly  a first step of reverse transcription RT SuperScript III  Thermo Fisher  Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT  primers were removed with an exonuclease ExoI NEB  Cat#: M0293L  and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit  NEB  Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit  NEB  Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher  Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher  Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase  Agilent  Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix  Roche Diagnostics  Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and \u00df actin  DNA quality control using a TapeStation  Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP592701", null, null, "TORCQ_2021_S0_R1_001.fastq.gz TORCQ_2021_S0_R2_001.fastq.gz", "fastq fastq", 45817068160.0, 602856160.0, "GSM9052755 r1", "0:56 1:20", "A:12324583812;C:8979463244;G:11486707902;T:13012728622;N:13584580", 56, 20, null, null, 12324583812, 8979463244, 11486707902, 13012728622, 13584580, "SRX29213467", "SRS25409912", "SRA2151098", "Institut Pasteur", "Institut Pasteur", null, null, null, null, null, null, null, null, null, null, null, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "marsseq", null, "France", "2025-06-17", "Larval", "Larval", "Blood", "Hematopoietic System"], [36254, "SRR34017906", "SRX29213467", "SRS25409912", "SRP592701", "PRJNA1278741", "Single cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches [scRNA Seq]", "GSE300039", "Transcriptome Analysis", "Hematopoietic stem cells HSCs and more committed progenitors collectively referred to as HSPCs emerge from vessels during development  via Endothelial to Hematopoietic Transition EHT. Recently  using the zebrafish embryo  we showed that two EHT cell types emerge from the dorsal aorta  raising the question of their subsequent fate. To address this issue  we established a complex pipeline based on single cell photoconversion and transgenic lines to characterize the abilities of EHT cell progenies to conquer hematopoietic organs and to obtain their transcriptomic profiles. We show that the two EHT cell types lead to partly differentially fated cells  with significant differences in thymus colonization and T lymphoid lineage commitment. In addition  we investigated implantation of HSPCs in niches  with the support of HSPC signatures gata2b and cd34/podocalyxin  retrieved from our single cell datasets. This revealed  at unprecedented resolution  the homing of HSPCs in niches of entire early larvae  including the pronephros  the sub aortic and caudal regions  as well as the area contacting the supra intestinal artery. Our work provides new insights on fundamental aspects of HSPC fate acquisition  from their emergence to their homing in specific niches. Overall design: Single cell transcriptomics analysis of newly born hematopoietic stem and progenitor cells. This dataset comprises progenies of cells photoconverted at 2dpf and sorted by FACS at 5dpf  using the Tgkdrl:nls kikume transgenic line  as well as sorted FACS hematopoietic cells from transgenic reporter lines  namely from the Tgrunx1+23:eGFP and the outcross of the Tgcd41:eGFP and Tggata2b:RFP lines. Larvae were collected post dissection separating the rostral  anterior and posterior region along a transversal section at the posterior limit of the elongated yolk and at the posterior limit of the swim bladder  dissociation and sorting using a BD FACS AriaIII cell sorter. Progenies of photoconverted cells comprise progenies of single EHT photoconversion either EHT pol+ or EHT pol  or whole hemogenic endothelium photoconversion. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019.", null, "pubmed:40501392", null, "5 dpf hematopoietic zebrafish cells  session 1", "GSM9052755", null, "tissue:sorted hematopoietic cells|cell type:sorted hematopoietic cells|geo loc name:missing|collection date:missing", "5 dpf hematopoietic zebrafish cells  session 1", "Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019 Assembly: zebrafish genome Lawson lab version 4.3.2. Supplementary files format and content: Tab separated value files", "sorted hematopoietic cells", null, "Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al.  2018; Manoli and Driever  2012; Samsa et al.  2016. All steps were performed with cooled solutions 4\u00b0C  and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly  5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine  at a final concentration of 640 \u00b5g/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4\u00b0C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies  Cat#: 12605 010 for 10 min on ice  with gentle pipetting every 3 mins  first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g  before the TrypLE was removed and the cells were resuspended in 500 \u00b5l FACSmax medium Genlantis  Cat#: T200100. Ultimately  samples were passed through a 40 \u03bcm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 \u00b5l of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples  gating was done on SSC A vs. FSC A to collect cells  then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher  Cat#: D15106. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019. Briefly  a first step of reverse transcription RT SuperScript III  Thermo Fisher  Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT  primers were removed with an exonuclease ExoI NEB  Cat#: M0293L  and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit  NEB  Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit  NEB  Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher  Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher  Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase  Agilent  Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix  Roche Diagnostics  Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and \u00df actin  DNA quality control using a TapeStation  Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.", null, "cell type:sorted hematopoietic cells", "GSM9052755", "GSM9052755: 5 dpf hematopoietic zebrafish cells  session 1; Danio rerio; RNA Seq", "GSM9052755 r1", "GSM9052755", "1", "Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al.  2018; Manoli and Driever  2012; Samsa et al.  2016. All steps were performed with cooled solutions 4\u00b0C  and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly  5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine  at a final concentration of 640 \u00b5g/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4\u00b0C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies  Cat#: 12605 010 for 10 min on ice  with gentle pipetting every 3 mins  first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g  before the TrypLE was removed and the cells were resuspended in 500 \u00b5l FACSmax medium Genlantis  Cat#: T200100. Ultimately  samples were passed through a 40 \u03bcm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 \u00b5l of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples  gating was done on SSC A vs. FSC A to collect cells  then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher  Cat#: D15106. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019. Briefly  a first step of reverse transcription RT SuperScript III  Thermo Fisher  Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT  primers were removed with an exonuclease ExoI NEB  Cat#: M0293L  and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit  NEB  Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit  NEB  Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher  Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher  Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase  Agilent  Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix  Roche Diagnostics  Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and \u00df actin  DNA quality control using a TapeStation  Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP592701", null, null, "TORCQ_2021_S0_R1_001_small.fastq.gz TORCQ_2021_S0_R2_001_small.fastq.gz", "fastq fastq", 190000.0, 2500.0, "GSM9052755 r2", "0:56 1:20", "A:50399;C:36081;G:47775;T:53618;N:2127", 56, 20, null, null, 50399, 36081, 47775, 53618, 2127, "SRX29213467", "SRS25409912", "SRA2151098", "Institut Pasteur", "Institut Pasteur", null, null, null, null, null, null, null, null, null, null, null, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "marsseq", null, "France", "2025-06-17", "Larval", "Larval", "Blood", "Hematopoietic 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. 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, "BC2_S0_R1_001.fastq.gz BC2_S0_R2_001.fastq.gz", "fastq fastq", 4158365400.0, 46204060.0, "GSM5910459 r1", "0:75 1:15", "A:1056133752;C:954371027;G:1117373354;T:1029764959;N:722308", 75, 15, null, null, 1056133752, 954371027, 1117373354, 1029764959, 722308, "SRX14248906", "SRS12068874", "SRA1376737", "Weizmann Institute of Science", "Department of Biological Regulation, Weizmann Institute of Science", 2, 0.76282, 0.0, 0.2382, 0.0, 0.87158, 1.0, 0.53888, 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"], [68658, "SRR18097959", "SRX14248905", "SRS12068873", "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 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. 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", "GSM5910458", "GSM5910458: Immature fin ECs plate1; Danio rerio; RNA Seq", "GSM5910458 r1", "GSM5910458", "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, "BC1_S0_R1_001.fastq.gz BC1_S0_R2_001.fastq.gz", "fastq fastq", 4284501750.0, 47605575.0, "GSM5910458 r1", "0:75 1:15", "A:1172578653;C:976724863;G:1071723716;T:1062724053;N:750465", 75, 15, null, null, 1172578653, 976724863, 1071723716, 1062724053, 750465, "SRX14248905", "SRS12068873", "SRA1376737", "Weizmann Institute of Science", "Department of Biological Regulation, Weizmann Institute of Science", 2, 0.73652, 0.0, 0.20176, 0.0, 0.86622, 1.0, 0.66697, 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"], [69988, "SRR19217299", "SRX15281308", "SRS13012753", "SRP375342", "PRJNA838481", "Neural plate progenitors give rise to both anterior and posterior pituitary cells", "GSE203075", "Transcriptome Analysis", "The pituitary is the master neuroendocrine tissue  which regulates body homeostasis. It consists of the adenohypophysis AH  which harbors hormones producing cells and the neurohypophysis NH  which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al.  2020. However  the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al.  2014  we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries  which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf  5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.", null, "pubmed:37683631", null, "AB9278", "GSM6153483", null, "source name:Neurohypophysis enriched cells|strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:7 month|geo loc name:missing|collection date:missing", "AB9278", "bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header  delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data  allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al.  2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=\"LogNormalize\"  scale.factor= 10000 and ScaleData vars.to.regress = c\"nCount RNA\"  \"percent.mito\". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = \"pca\"  resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster", "Neurohypophysis enriched cells", "5ul of 4.6mM \u03b2 Ala Lys N\u03b5 AMCA Biotrend #BP0352 was injected into 37 dpf juvenile  or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours  the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.", "37 dpf  5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.", "strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:7 month", "GSM6153483", "GSM6153483: AB9278; Danio rerio; RNA Seq", "GSM6153483 r1", "GSM6153483", "1", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP375342", null, "loader:fastq load.py", "AB9278_SB390_R1_01.fastq.gz AB9278_SB390_R2_01.fastq.gz", "fastq fastq", 1259447780.0, 11770540.0, "GSM6153483 r1", "0:92 1:15", "A:305608913;C:313550706;G:363197186;T:277079546;N:11429", 92, 15, null, null, 305608913, 313550706, 363197186, 277079546, 11429, "SRX15281308", "SRS13012753", "SRA1420605", "Molecular Cell Biology, Weizmann Institute of Science", "Molecular Cell Biology, Weizmann Institute of Science", 2, 0.94767, 0.0, 0.32091, 0.0, 0.89796, 1.0, 0.7545, null, 92, 15, "B", "T", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2022-05-16", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [69989, "SRR19217300", "SRX15281307", "SRS13012752", "SRP375342", "PRJNA838481", "Neural plate progenitors give rise to both anterior and posterior pituitary cells", "GSE203075", "Transcriptome Analysis", "The pituitary is the master neuroendocrine tissue  which regulates body homeostasis. It consists of the adenohypophysis AH  which harbors hormones producing cells and the neurohypophysis NH  which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al.  2020. However  the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al.  2014  we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries  which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf  5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.", null, "pubmed:37683631", null, "AB9277", "GSM6153482", null, "source name:Neurohypophysis enriched cells|strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:7 month|geo loc name:missing|collection date:missing", "AB9277", "bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header  delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data  allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al.  2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=\"LogNormalize\"  scale.factor= 10000 and ScaleData vars.to.regress = c\"nCount RNA\"  \"percent.mito\". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = \"pca\"  resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster", "Neurohypophysis enriched cells", "5ul of 4.6mM \u03b2 Ala Lys N\u03b5 AMCA Biotrend #BP0352 was injected into 37 dpf juvenile  or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours  the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.", "37 dpf  5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.", "strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:7 month", "GSM6153482", "GSM6153482: AB9277; Danio rerio; RNA Seq", "GSM6153482 r1", "GSM6153482", "1", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP375342", null, "loader:fastq load.py", "AB9277_SB390_R1_01.fastq.gz AB9277_SB390_R2_01.fastq.gz", "fastq fastq", 1130776107.0, 10568001.0, "GSM6153482 r1", "0:92 1:15", "A:288600700;C:269726443;G:310844405;T:261594352;N:10207", 92, 15, null, null, 288600700, 269726443, 310844405, 261594352, 10207, "SRX15281307", "SRS13012752", "SRA1420605", "Molecular Cell Biology, Weizmann Institute of Science", "Molecular Cell Biology, Weizmann Institute of Science", 2, 0.94379, 0.0, 0.28638, 0.0, 0.86415, 1.0, 0.63321, null, 92, 15, "B", "T", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2022-05-16", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [69990, "SRR19217301", "SRX15281306", "SRS13012751", "SRP375342", "PRJNA838481", "Neural plate progenitors give rise to both anterior and posterior pituitary cells", "GSE203075", "Transcriptome Analysis", "The pituitary is the master neuroendocrine tissue  which regulates body homeostasis. It consists of the adenohypophysis AH  which harbors hormones producing cells and the neurohypophysis NH  which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al.  2020. However  the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al.  2014  we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries  which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf  5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.", null, "pubmed:37683631", null, "AB9280", "GSM6153481", null, "source name:Neurohypophysis enriched cells|strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:5 month|geo loc name:missing|collection date:missing", "AB9280", "bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header  delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data  allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al.  2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=\"LogNormalize\"  scale.factor= 10000 and ScaleData vars.to.regress = c\"nCount RNA\"  \"percent.mito\". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = \"pca\"  resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster", "Neurohypophysis enriched cells", "5ul of 4.6mM \u03b2 Ala Lys N\u03b5 AMCA Biotrend #BP0352 was injected into 37 dpf juvenile  or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours  the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.", "37 dpf  5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.", "strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:5 month", "GSM6153481", "GSM6153481: AB9280; Danio rerio; RNA Seq", "GSM6153481 r1", "GSM6153481", "1", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP375342", null, "loader:fastq load.py", "AB9280_SB390_R1_01.fastq.gz AB9280_SB390_R2_01.fastq.gz", "fastq fastq", 1172966528.0, 10962304.0, "GSM6153481 r1", "0:92 1:15", "A:311089180;C:274626206;G:310304031;T:276936052;N:11059", 92, 15, null, null, 311089180, 274626206, 310304031, 276936052, 11059, "SRX15281306", "SRS13012751", "SRA1420605", "Molecular Cell Biology, Weizmann Institute of Science", "Molecular Cell Biology, Weizmann Institute of Science", 2, 0.92936, 0.0, 0.23628, 0.0, 0.86147, 1.0, 0.74656, null, 92, 15, "B", "T", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2022-05-16", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [69991, "SRR19217302", "SRX15281305", "SRS13012750", "SRP375342", "PRJNA838481", "Neural plate progenitors give rise to both anterior and posterior pituitary cells", "GSE203075", "Transcriptome Analysis", "The pituitary is the master neuroendocrine tissue  which regulates body homeostasis. It consists of the adenohypophysis AH  which harbors hormones producing cells and the neurohypophysis NH  which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al.  2020. However  the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al.  2014  we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries  which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf  5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.", null, "pubmed:37683631", null, "AB9279", "GSM6153480", null, "source name:Neurohypophysis enriched cells|strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:5 month|geo loc name:missing|collection date:missing", "AB9279", "bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header  delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data  allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al.  2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=\"LogNormalize\"  scale.factor= 10000 and ScaleData vars.to.regress = c\"nCount RNA\"  \"percent.mito\". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = \"pca\"  resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster", "Neurohypophysis enriched cells", "5ul of 4.6mM \u03b2 Ala Lys N\u03b5 AMCA Biotrend #BP0352 was injected into 37 dpf juvenile  or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours  the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.", "37 dpf  5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.", "strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:5 month", "GSM6153480", "GSM6153480: AB9279; Danio rerio; RNA Seq", "GSM6153480 r1", "GSM6153480", "1", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP375342", null, "loader:fastq load.py", "AB9279_SB390_R1_01.fastq.gz AB9279_SB390_R2_01.fastq.gz", "fastq fastq", 1383147163.0, 12926609.0, "GSM6153480 r1", "0:92 1:15", "A:364575971;C:320901229;G:367626618;T:330030659;N:12686", 92, 15, null, null, 364575971, 320901229, 367626618, 330030659, 12686, "SRX15281305", "SRS13012750", "SRA1420605", "Molecular Cell Biology, Weizmann Institute of Science", "Molecular Cell Biology, Weizmann Institute of Science", 2, 0.92462, 0.0, 0.26743, 0.0, 0.8493, 1.0, 0.74133, null, 92, 15, "B", "T", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2022-05-16", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [69992, "SRR19217303", "SRX15281304", "SRS13012749", "SRP375342", "PRJNA838481", "Neural plate progenitors give rise to both anterior and posterior pituitary cells", "GSE203075", "Transcriptome Analysis", "The pituitary is the master neuroendocrine tissue  which regulates body homeostasis. It consists of the adenohypophysis AH  which harbors hormones producing cells and the neurohypophysis NH  which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al.  2020. However  the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al.  2014  we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries  which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf  5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.", null, "pubmed:37683631", null, "AB7418", "GSM6153479", null, "source name:Neurohypophysis enriched cells|strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:37 dpf loc name:missing|collection date:missing", "AB7418", "bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header  delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data  allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al.  2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=\"LogNormalize\"  scale.factor= 10000 and ScaleData vars.to.regress = c\"nCount RNA\"  \"percent.mito\". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = \"pca\"  resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster", "Neurohypophysis enriched cells", "5ul of 4.6mM \u03b2 Ala Lys N\u03b5 AMCA Biotrend #BP0352 was injected into 37 dpf juvenile  or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours  the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.", "37 dpf  5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.", "strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:37 dpf", "GSM6153479", "GSM6153479: AB7418; Danio rerio; RNA Seq", "GSM6153479 r1", "GSM6153479", "1", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP375342", null, null, "AB7418_SB350_S35_R1_001.fastq.gz AB7418_SB350_S35_R2_001.fastq.gz", "fastq fastq", 2468773944.0, 29390166.0, "GSM6153479 r1", "0:69 1:15", "A:764359919;C:520031317;G:592699381;T:591594655;N:88672", 69, 15, null, null, 764359919, 520031317, 592699381, 591594655, 88672, "SRX15281304", "SRS13012749", "SRA1420605", "Molecular Cell Biology, Weizmann Institute of Science", "Molecular Cell Biology, Weizmann Institute of Science", 2, 0.85786, 0.0, 0.15143, 0.0, 0.84885, 1.0, 0.67021, null, 69, 15, "B", "T", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2022-05-16", "Juvenile", "Juvenile", "Pituitary Gland", "Endocrine System"], [69993, "SRR19217304", "SRX15281303", "SRS13012748", "SRP375342", "PRJNA838481", "Neural plate progenitors give rise to both anterior and posterior pituitary cells", "GSE203075", "Transcriptome Analysis", "The pituitary is the master neuroendocrine tissue  which regulates body homeostasis. It consists of the adenohypophysis AH  which harbors hormones producing cells and the neurohypophysis NH  which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al.  2020. However  the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al.  2014  we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries  which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf  5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.", null, "pubmed:37683631", null, "AB7417", "GSM6153478", null, "source name:Neurohypophysis enriched cells|strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:37 dpf loc name:missing|collection date:missing", "AB7417", "bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header  delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data  allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al.  2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=\"LogNormalize\"  scale.factor= 10000 and ScaleData vars.to.regress = c\"nCount RNA\"  \"percent.mito\". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = \"pca\"  resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster", "Neurohypophysis enriched cells", "5ul of 4.6mM \u03b2 Ala Lys N\u03b5 AMCA Biotrend #BP0352 was injected into 37 dpf juvenile  or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours  the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.", "37 dpf  5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.", "strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:37 dpf", "GSM6153478", "GSM6153478: AB7417; Danio rerio; RNA Seq", "GSM6153478 r1", "GSM6153478", "1", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP375342", null, null, "AB7417_SB350_S24_R1_001.fastq.gz AB7417_SB350_S24_R2_001.fastq.gz", "fastq fastq", 2586526488.0, 30791982.0, "GSM6153478 r1", "0:69 1:15", "A:833353097;C:525447349;G:601496569;T:626135990;N:93483", 69, 15, null, null, 833353097, 525447349, 601496569, 626135990, 93483, "SRX15281303", "SRS13012748", "SRA1420605", "Molecular Cell Biology, Weizmann Institute of Science", "Molecular Cell Biology, Weizmann Institute of Science", 2, 0.84125, 0.0, 0.10717, 0.0, 0.84768, 1.0, 0.63154, null, 69, 15, "B", "T", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2022-05-16", "Juvenile", "Juvenile", "Pituitary Gland", "Endocrine System"]], "truncated": false, "filtered_table_rows_count": 24, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"experiment.library_strategy\" = :p0 and \"experiment.platform\" = :p1 and \"technology\" = :p2 order by rowid limit 101", "params": {"p0": "RNA-Seq", "p1": "ILLUMINA", "p2": "marsseq"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_strategy=RNA-Seq&experiment.platform=ILLUMINA&technology=marsseq", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 24, "toggle_url": 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true, "query_ms": 156.9893459964078}