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 25302,SRR25793493,SRX21515745,SRS18742910,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,Single cell Pr1phros ADULT miR 144 mutant Danio rerio,miR 144,,isolate:miR 144 mutant|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:blood|BioSampleModel:Model organism or animal,,,,,,,,,Single cell Pr1phros ADULT miR 144 mutant Danio rerio,CD 144 1,CD 144 1,Single cell library cloning was done with 10X Genomics,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,unspecified,PAIRED,ILLUMINA,NextSeq 2000,,SRP457465,,,CD_144_1_S3_R1.fastq CD_144_1_S3_R2.fastq,fastq fastq,12899093774.0,108395746.0,CD 144 1 S3 R1.fastq,0:28 1:91,A:3225260764;C:3211986177;G:3151471558;T:3308055659;N:2319616,28,91,,,3225260764,3211986177,3151471558,3308055659,2319616,SRX21515745,SRS18742910,SRA1701829,University of East Anglia|Biological Sciences,University of East Anglia,2,0.00483,0.97382,0.00157,0.05913,0.99439,0.86815,0.46634,0.45907,28,91,T,B,sc-like readlen,illumina,nextseq_v2,unknown,unknown,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-30,Adult,Adult,Blood,Hematopoietic System 25303,SRR25793494,SRX21515744,SRS18742909,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,Single cell Pr1phros ADULT Wild type Danio rerio,WT,,isolate:Wildtype|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:blood|BioSampleModel:Model organism or animal,,,,,,,,,Single cell Pr1phros ADULT Wild type Danio rerio,CD wt 1,CD wt 1,Single cell library cloning was done with 10X Genomics,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,unspecified,PAIRED,ILLUMINA,NextSeq 2000,,SRP457465,,,CD_wt_1_S2_R1.fastq CD_wt_1_S2_R2.fastq,fastq fastq,12715533299.0,106853221.0,CD wt 1 S2 R1.fastq,0:28 1:91,A:3324705878;C:3042843364;G:3105568183;T:3240105528;N:2310346,28,91,,,3324705878,3042843364,3105568183,3240105528,2310346,SRX21515744,SRS18742909,SRA1701829,University of East Anglia|Biological Sciences,University of East Anglia,2,0.00593,0.93177,0.00191,0.09596,0.99257,0.84394,0.42447,0.4869,28,91,T,B,sc-like readlen,illumina,nextseq_v2,unknown,unknown,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-30,Adult,Adult,Blood,Hematopoietic System 29175,SRR27292304,SRX22969963,SRS19936063,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222 200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin 1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2 100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris singles versus doublets live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Burned Larval Zebrafish 48 hours post burn,GSM7982886,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing,Burned Larval Zebrafish 48 hours post burn,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn,GSM7982886,GSM7982886: Burned Larval Zebrafish 48 hours post burn; Danio rerio; RNA Seq,GSM7982886 r1,GSM7982886,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,Burn-48hpb_S5_L001_R2_001.fastq.gz Burn-48hpb_S5_L001_R1_001.fastq.gz,fastq fastq,20874980529.0,178418637.0,GSM7982886 r1,0:28 1:89,A:5945091269;C:4392590896;G:4497688824;T:6035946283;N:3663257,28,89,,,5945091269,4392590896,4497688824,6035946283,3663257,SRX22969963,SRS19936063,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.00573,0.91666,0.00222,0.19474,0.9931,0.79306,0.42082,0.53801,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System 29176,SRR27292305,SRX22969963,SRS19936063,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222 200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin 1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2 100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris singles versus doublets live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Burned Larval Zebrafish 48 hours post burn,GSM7982886,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing,Burned Larval Zebrafish 48 hours post burn,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn,GSM7982886,GSM7982886: Burned Larval Zebrafish 48 hours post burn; Danio rerio; RNA Seq,GSM7982886 r1,GSM7982886,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,Burn-48hpb_S5_L002_R1_001.fastq.gz Burn-48hpb_S5_L002_R2_001.fastq.gz,fastq fastq,20022973425.0,171136525.0,GSM7982886 r2,0:28 1:89,A:5709681181;C:4208386174;G:4307510275;T:5796282368;N:1113427,28,89,,,5709681181,4208386174,4307510275,5796282368,1113427,SRX22969963,SRS19936063,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.00547,0.9154,0.00202,0.1955,0.99283,0.79423,0.39307,0.53427,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System 29177,SRR27292306,SRX22969962,SRS19936064,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222 200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin 1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2 100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris singles versus doublets live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Burned Larval Zebrafish 24 hours post burn,GSM7982885,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing,Burned Larval Zebrafish 24 hours post burn,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn,GSM7982885,GSM7982885: Burned Larval Zebrafish 24 hours post burn; Danio rerio; RNA Seq,GSM7982885 r1,GSM7982885,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,Burn-24hpb_S2_L001_R1_001.fastq.gz Burn-24hpb_S2_L001_R2_001.fastq.gz,fastq fastq,9782870058.0,83614274.0,GSM7982885 r1,0:28 1:89,A:2744737668;C:2140848416;G:2249400157;T:2645170677;N:2713140,28,89,,,2744737668,2140848416,2249400157,2645170677,2713140,SRX22969962,SRS19936064,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.00752,0.92059,0.00244,0.16143,0.98944,0.82929,0.44176,0.54525,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System 29178,SRR27292307,SRX22969962,SRS19936064,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222 200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin 1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2 100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris singles versus doublets live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Burned Larval Zebrafish 24 hours post burn,GSM7982885,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing,Burned Larval Zebrafish 24 hours post burn,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn,GSM7982885,GSM7982885: Burned Larval Zebrafish 24 hours post burn; Danio rerio; RNA Seq,GSM7982885 r1,GSM7982885,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,Burn-24hpb_S2_L002_R2_001.fastq.gz Burn-24hpb_S2_L002_R1_001.fastq.gz,fastq fastq,9861989202.0,84290506.0,GSM7982885 r2,0:28 1:89,A:2769268861;C:2158644227;G:2263475493;T:2669311436;N:1289185,28,89,,,2769268861,2158644227,2263475493,2669311436,1289185,SRX22969962,SRS19936064,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.0076,0.9197,0.00232,0.16162,0.98995,0.82852,0.43786,0.55256,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System 29179,SRR27292308,SRX22969961,SRS19936062,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222 200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin 1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2 100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris singles versus doublets live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Burned Larval Zebrafish 6 hours post burn,GSM7982884,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing,Burned Larval Zebrafish 6 hours post burn,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn,GSM7982884,GSM7982884: Burned Larval Zebrafish 6 hours post burn; Danio rerio; RNA Seq,GSM7982884 r1,GSM7982884,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,Burn-6hpb_S7_L001_R1_001.fastq.gz Burn-6hpb_S7_L001_R2_001.fastq.gz,fastq fastq,12475938384.0,106631952.0,GSM7982884 r1,0:28 1:89,A:3401989108;C:2878275107;G:3114945415;T:3078525361;N:2203393,28,89,,,3401989108,2878275107,3114945415,3078525361,2203393,SRX22969961,SRS19936062,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.01053,0.89396,0.00429,0.18315,0.99458,0.85756,0.34876,0.58728,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System 29180,SRR27292309,SRX22969961,SRS19936062,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222 200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin 1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2 100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris singles versus doublets live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Burned Larval Zebrafish 6 hours post burn,GSM7982884,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing,Burned Larval Zebrafish 6 hours post burn,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn,GSM7982884,GSM7982884: Burned Larval Zebrafish 6 hours post burn; Danio rerio; RNA Seq,GSM7982884 r1,GSM7982884,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,Burn-6hpb_S7_L002_R1_001.fastq.gz Burn-6hpb_S7_L002_R2_001.fastq.gz,fastq fastq,11874083247.0,101487891.0,GSM7982884 r2,0:28 1:89,A:3243501055;C:2735412615;G:2958387721;T:2936117380;N:664476,28,89,,,3243501055,2735412615,2958387721,2936117380,664476,SRX22969961,SRS19936062,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.01063,0.89389,0.00439,0.18047,0.99403,0.85878,0.36393,0.54831,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System 29181,SRR27292310,SRX22969960,SRS19936061,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222 200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin 1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2 100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris singles versus doublets live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Unwounded Larval Zebrafish 5 dpf,GSM7982883,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing,Unwounded Larval Zebrafish 5 dpf,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded,GSM7982883,GSM7982883: Unwounded Larval Zebrafish 5 dpf Danio rerio; RNA Seq,GSM7982883 r1,GSM7982883,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,WT-5dpf_S6_L001_R2_001.fastq.gz WT-5dpf_S6_L001_R1_001.fastq.gz,fastq fastq,31813158312.0,271907336.0,GSM7982883 r1,0:28 1:89,A:8991313503;C:6911976524;G:7105775004;T:8798521232;N:5572049,28,89,,,8991313503,6911976524,7105775004,8798521232,5572049,SRX22969960,SRS19936061,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.00661,0.92343,0.00245,0.19293,0.99255,0.81379,0.35935,0.54818,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System 29182,SRR27292311,SRX22969960,SRS19936061,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222 200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin 1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2 100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris singles versus doublets live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Unwounded Larval Zebrafish 5 dpf,GSM7982883,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing,Unwounded Larval Zebrafish 5 dpf,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded,GSM7982883,GSM7982883: Unwounded Larval Zebrafish 5 dpf Danio rerio; RNA Seq,GSM7982883 r1,GSM7982883,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,WT-5dpf_S6_L002_R1_001.fastq.gz WT-5dpf_S6_L002_R2_001.fastq.gz,fastq fastq,30524386113.0,260892189.0,GSM7982883 r2,0:28 1:89,A:8637605077;C:6625244702;G:6807369409;T:8452468968;N:1697957,28,89,,,8637605077,6625244702,6807369409,8452468968,1697957,SRX22969960,SRS19936061,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.00648,0.92418,0.00233,0.19549,0.99241,0.81444,0.37733,0.54674,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System 29183,SRR27292312,SRX22969959,SRS19936060,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222 200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin 1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2 100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris singles versus doublets live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Unwounded Larval Zebrafish 4 dpf,GSM7982882,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing,Unwounded Larval Zebrafish 4 dpf,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded,GSM7982882,GSM7982882: Unwounded Larval Zebrafish 4 dpf Danio rerio; RNA Seq,GSM7982882 r1,GSM7982882,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,WT-4dpf_S1_L001_R1_001.fastq.gz WT-4dpf_S1_L001_R2_001.fastq.gz,fastq fastq,12682286721.0,108395613.0,GSM7982882 r1,0:28 1:89,A:3575375325;C:2777398557;G:2900088646;T:3425909511;N:3514682,28,89,,,3575375325,2777398557,2900088646,3425909511,3514682,SRX22969959,SRS19936060,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.00505,0.92112,0.00185,0.16865,0.99257,0.8258,0.38216,0.5512,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System 29184,SRR27292313,SRX22969959,SRS19936060,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222 200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin 1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2 100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris singles versus doublets live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Unwounded Larval Zebrafish 4 dpf,GSM7982882,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing,Unwounded Larval Zebrafish 4 dpf,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded,GSM7982882,GSM7982882: Unwounded Larval Zebrafish 4 dpf Danio rerio; RNA Seq,GSM7982882 r1,GSM7982882,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,WT-4dpf_S1_L002_R2_001.fastq.gz WT-4dpf_S1_L002_R1_001.fastq.gz,fastq fastq,12832453413.0,109679089.0,GSM7982882 r2,0:28 1:89,A:3620789787;C:2810897812;G:2929508681;T:3469577031;N:1680102,28,89,,,3620789787,2810897812,2929508681,3469577031,1680102,SRX22969959,SRS19936060,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.0052,0.92355,0.00192,0.16775,0.99263,0.8253,0.37089,0.55115,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System 29185,SRR27292314,SRX22969958,SRS19936059,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222 200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin 1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2 100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris singles versus doublets live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Unwounded Larval Zebrafish 3 dpf,GSM7982881,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing,Unwounded Larval Zebrafish 3 dpf,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded,GSM7982881,GSM7982881: Unwounded Larval Zebrafish 3 dpf Danio rerio; RNA Seq,GSM7982881 r1,GSM7982881,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,WT-3dpf_S4_L001_R1_001.fastq.gz WT-3dpf_S4_L001_R2_001.fastq.gz,fastq fastq,7586138430.0,64838790.0,GSM7982881 r1,0:28 1:89,A:2101749534;C:1692875352;G:1784872358;T:2005308370;N:1332816,28,89,,,2101749534,1692875352,1784872358,2005308370,1332816,SRX22969958,SRS19936059,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.00976,0.92096,0.00368,0.18077,0.99356,0.83875,0.3661,0.59073,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System 29186,SRR27292315,SRX22969958,SRS19936059,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222 200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin 1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2 100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris singles versus doublets live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Unwounded Larval Zebrafish 3 dpf,GSM7982881,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing,Unwounded Larval Zebrafish 3 dpf,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded,GSM7982881,GSM7982881: Unwounded Larval Zebrafish 3 dpf Danio rerio; RNA Seq,GSM7982881 r1,GSM7982881,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,WT-3dpf_S4_L002_R1_001.fastq.gz WT-3dpf_S4_L002_R2_001.fastq.gz,fastq fastq,7258692168.0,62040104.0,GSM7982881 r2,0:28 1:89,A:2013529524;C:1617959197;G:1704796898;T:1922004726;N:401823,28,89,,,2013529524,1617959197,1704796898,1922004726,401823,SRX22969958,SRS19936059,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.00949,0.92207,0.00359,0.18081,0.99375,0.83751,0.37347,0.55889,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System 35485,SRR32834031,SRX28117245,SRS24473023,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells rag1 crispant R848 treated,GSM8864273,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|genotype:rag1 mosaic mutant|treatment:Resiquimod R848 treated|geo loc name:missing|collection date:missing,mCherry cells rag1 crispant R848 treated,For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions at 28C,cell type:Hematopoietic & Immune Cells|genotype:rag1 mosaic mutant|treatment:Resiquimod R848 treated,GSM8864273,GSM8864273: mCherry cells rag1 crispant R848 treated; Danio rerio; RNA Seq,GSM8864273 r1,GSM8864273,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options: readTypes=TBTT read1PairFiles=Rag1 crispant with R848 S64 L005 R1 001.fastq.gz read2PairFiles=Rag1 crispant with R848 S64 L005 R2 001.fastq.gz read3PairFiles=Rag1 crispant with R848 S64 L005 I1 001.fastq.gz read4PairFiles=Rag1 crispant with R848 S64 L005 I2 001.fastq.gz,Rag1_crispant_with_R848_S64_L005_I1_001.fastq.gz Rag1_crispant_with_R848_S64_L005_I2_001.fastq.gz Rag1_crispant_with_R848_S64_L005_R1_001.fastq.gz Rag1_crispant_with_R848_S64_L005_R2_001.fastq.gz,fastq fastq fastq fastq,51690121264.0,371871376.0,GSM8864273 r1,0:28 1:91 2:10 3:10,A:9268291738;C:7690563124;G:8398909329;T:8480309041;N:2221984,28,91,10,10,9268291738,7690563124,8398909329,8480309041,2221984,SRX28117245,SRS24473023,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System 35486,SRR32834032,SRX28117244,SRS24473025,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells slc24a5 crispant R848 treated,GSM8864272,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|genotype:slc24a5 mosaic mutant|treatment:Resiquimod R848 treated|geo loc name:missing|collection date:missing,mCherry cells slc24a5 crispant R848 treated,For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions at 28C,cell type:Hematopoietic & Immune Cells|genotype:slc24a5 mosaic mutant|treatment:Resiquimod R848 treated,GSM8864272,GSM8864272: mCherry cells slc24a5 crispant R848 treated; Danio rerio; RNA Seq,GSM8864272 r1,GSM8864272,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options: readTypes=TBTT read1PairFiles=slc24a5 crispant with R848 S62 L005 R1 001.fastq.gz read2PairFiles=slc24a5 crispant with R848 S62 L005 R2 001.fastq.gz read3PairFiles=slc24a5 crispant with R848 S62 L005 I1 001.fastq.gz read4PairFiles=slc24a5 crispant with R848 S62 L005 I2 001.fastq.gz,slc24a5_crispant_with_R848_S62_L005_I1_001.fastq.gz slc24a5_crispant_with_R848_S62_L005_I2_001.fastq.gz slc24a5_crispant_with_R848_S62_L005_R1_001.fastq.gz slc24a5_crispant_with_R848_S62_L005_R2_001.fastq.gz,fastq fastq fastq fastq,67359016638.0,484597242.0,GSM8864272 r1,0:28 1:91 2:10 3:10,A:12101967291;C:10017190111;G:10977547337;T:10998758556;N:2885727,28,91,10,10,12101967291,10017190111,10977547337,10998758556,2885727,SRX28117244,SRS24473025,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System 35487,SRR32834033,SRX28117243,SRS24473024,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells rag1 crispant,GSM8864271,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|genotype:rag1 mosaic mutant|geo loc name:missing|collection date:missing,mCherry cells rag1 crispant,For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions at 28C,cell type:Hematopoietic & Immune Cells|genotype:rag1 mosaic mutant,GSM8864271,GSM8864271: mCherry cells rag1 crispant; Danio rerio; RNA Seq,GSM8864271 r1,GSM8864271,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options: readTypes=TBTT read1PairFiles=Rag1 crispant S63 L005 R1 001.fastq.gz read2PairFiles=Rag1 crispant S63 L005 R2 001.fastq.gz read3PairFiles=Rag1 crispant S63 L005 I1 001.fastq.gz read4PairFiles=Rag1 crispant S63 L005 I2 001.fastq.gz,Rag1_crispant_S63_L005_I1_001.fastq.gz Rag1_crispant_S63_L005_I2_001.fastq.gz Rag1_crispant_S63_L005_R1_001.fastq.gz Rag1_crispant_S63_L005_R2_001.fastq.gz,fastq fastq fastq fastq,40550115550.0,291727450.0,GSM8864271 r1,0:28 1:91 2:10 3:10,A:7262987235;C:6078752458;G:6639990009;T:6563701562;N:1766686,28,91,10,10,7262987235,6078752458,6639990009,6563701562,1766686,SRX28117243,SRS24473024,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System 35488,SRR32834034,SRX28117242,SRS24473022,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells slc24a5 crispant,GSM8864270,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|genotype:slc24a5 mosaic mutant|geo loc name:missing|collection date:missing,mCherry cells slc24a5 crispant,For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions at 28C,cell type:Hematopoietic & Immune Cells|genotype:slc24a5 mosaic mutant,GSM8864270,GSM8864270: mCherry cells slc24a5 crispant; Danio rerio; RNA Seq,GSM8864270 r1,GSM8864270,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options: readTypes=TBTT read1PairFiles=slc24a5 crispant S61 L005 R1 001.fastq.gz read2PairFiles=slc24a5 crispant S61 L005 R2 001.fastq.gz read3PairFiles=slc24a5 crispant S61 L005 I1 001.fastq.gz read4PairFiles=slc24a5 crispant S61 L005 I2 001.fastq.gz,slc24a5_crispant_S61_L005_I1_001.fastq.gz slc24a5_crispant_S61_L005_I2_001.fastq.gz slc24a5_crispant_S61_L005_R1_001.fastq.gz slc24a5_crispant_S61_L005_R2_001.fastq.gz,fastq fastq fastq fastq,53500554564.0,384896076.0,GSM8864270 r1,0:28 1:91 2:10 3:10,A:9607899809;C:8061049626;G:8772491787;T:8581787300;N:2314394,28,91,10,10,9607899809,8061049626,8772491787,8581787300,2314394,SRX28117242,SRS24473022,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System 35489,SRR32834035,SRX28117241,SRS24473017,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells runx1 homozygous mutants,GSM8864269,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|genotype:runx1 homozygous|geo loc name:missing|collection date:missing,mCherry cells runx1 homozygous mutants,For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions at 28C,cell type:Hematopoietic & Immune Cells|genotype:runx1 homozygous,GSM8864269,GSM8864269: mCherry cells runx1 homozygous mutants; Danio rerio; RNA Seq,GSM8864269 r1,GSM8864269,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options: readTypes=TBTT read1PairFiles=Runx1 Homz Mutants earlyHSPC trace 6 dpf S2 L002 R1 001.fastq.gz read2PairFiles=Runx1 Homz Mutants earlyHSPC trace 6 dpf S2 L002 R2 001.fastq.gz read3PairFiles=Runx1 Homz Mutants earlyHSPC trace 6 dpf S2 L002 I1 001.fastq.gz read4PairFiles=Runx1 Homz Mutants earlyHSPC trace 6 dpf S2 L002 I2 001.fastq.gz,Runx1_Homz_Mutants_earlyHSPC_trace_6_dpf_S2_L002_I1_001.fastq.gz Runx1_Homz_Mutants_earlyHSPC_trace_6_dpf_S2_L002_I2_001.fastq.gz Runx1_Homz_Mutants_earlyHSPC_trace_6_dpf_S2_L002_R1_001.fastq.gz Runx1_Homz_Mutants_earlyHSPC_trace_6_dpf_S2_L002_R2_001.fastq.gz,fastq fastq fastq fastq,27845512960.0,87017228.0,GSM8864269 r1,0:150 1:150 2:10 3:10,A:4012440512;C:2615250336;G:3042659166;T:3381797139;N:437047,150,150,10,10,4012440512,2615250336,3042659166,3381797139,437047,SRX28117241,SRS24473017,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System 35490,SRR32834036,SRX28117240,SRS24473018,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells sibling controls,GSM8864268,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|genotype:wild type or runx1 heterozygous|geo loc name:missing|collection date:missing,mCherry cells sibling controls,For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions at 28C,cell type:Hematopoietic & Immune Cells|genotype:wild type or runx1 heterozygous,GSM8864268,GSM8864268: mCherry cells sibling controls; Danio rerio; RNA Seq,GSM8864268 r1,GSM8864268,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options: readTypes=TBTT read1PairFiles=Sibling Control earlyHSPC trace 6 dpf S1 L002 R1 001.fastq.gz read2PairFiles=Sibling Control earlyHSPC trace 6 dpf S1 L002 R2 001.fastq.gz read3PairFiles=Sibling Control earlyHSPC trace 6 dpf S1 L002 I1 001.fastq.gz read4PairFiles=Sibling Control earlyHSPC trace 6 dpf S1 L002 I2 001.fastq.gz,Sibling_Control_earlyHSPC_trace_6_dpf_S1_L002_I1_001.fastq.gz Sibling_Control_earlyHSPC_trace_6_dpf_S1_L002_I2_001.fastq.gz Sibling_Control_earlyHSPC_trace_6_dpf_S1_L002_R1_001.fastq.gz Sibling_Control_earlyHSPC_trace_6_dpf_S1_L002_R2_001.fastq.gz,fastq fastq fastq fastq,24953253760.0,77978918.0,GSM8864268 r1,0:150 1:150 2:10 3:10,A:3390875336;C:2571521800;G:2871954356;T:2862416982;N:69226,150,150,10,10,3390875336,2571521800,2871954356,2862416982,69226,SRX28117240,SRS24473018,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System 35491,SRR32834037,SRX28117239,SRS24473015,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells late HSPCs 10 dpf,GSM8864267,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells late HSPCs 10 dpf,For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions at 28C,cell type:Hematopoietic & Immune Cells,GSM8864267,GSM8864267: mCherry cells late HSPCs 10 dpf; Danio rerio; RNA Seq,GSM8864267 r1,GSM8864267,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options: readTypes=TBTT read1PairFiles=lateHSPC trace at 10dpf S1 L003 R1 001.fastq.gz read2PairFiles=lateHSPC trace at 10dpf S1 L003 R2 001.fastq.gz read3PairFiles=lateHSPC trace at 10dpf S1 L003 I1 001.fastq.gz read4PairFiles=lateHSPC trace at 10dpf S1 L003 I2 001.fastq.gz,lateHSPC_trace_at_10dpf_S1_L003_I1_001.fastq.gz lateHSPC_trace_at_10dpf_S1_L003_I2_001.fastq.gz lateHSPC_trace_at_10dpf_S1_L003_R1_001.fastq.gz lateHSPC_trace_at_10dpf_S1_L003_R2_001.fastq.gz,fastq fastq fastq fastq,49750537600.0,155470430.0,GSM8864267 r1,0:150 1:150 2:10 3:10,A:6695708919;C:5110107098;G:5648204020;T:5864962224;N:1582239,150,150,10,10,6695708919,5110107098,5648204020,5864962224,1582239,SRX28117239,SRS24473015,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System 35492,SRR32834038,SRX28117239,SRS24473015,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells late HSPCs 10 dpf,GSM8864267,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells late HSPCs 10 dpf,For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions at 28C,cell type:Hematopoietic & Immune Cells,GSM8864267,GSM8864267: mCherry cells late HSPCs 10 dpf; Danio rerio; RNA Seq,GSM8864267 r1,GSM8864267,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options: readTypes=TBTT read1PairFiles=lateHSPC trace at 10dpf S18 L002 R1 001.fastq.gz read2PairFiles=lateHSPC trace at 10dpf S18 L002 R2 001.fastq.gz read3PairFiles=lateHSPC trace at 10dpf S18 L002 I1 001.fastq.gz read4PairFiles=lateHSPC trace at 10dpf S18 L002 I2 001.fastq.gz,lateHSPC_trace_at_10dpf_S18_L002_I1_001.fastq.gz lateHSPC_trace_at_10dpf_S18_L002_I2_001.fastq.gz lateHSPC_trace_at_10dpf_S18_L002_R1_001.fastq.gz lateHSPC_trace_at_10dpf_S18_L002_R2_001.fastq.gz,fastq fastq fastq fastq,3818546250.0,27670625.0,GSM8864267 r2,0:28 1:90 2:10 3:10,A:716133237;C:554493684;G:608989896;T:610460128;N:279305,28,90,10,10,716133237,554493684,608989896,610460128,279305,SRX28117239,SRS24473015,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System 35493,SRR32834039,SRX28117238,SRS24473019,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells late HSPCs 6 dpf,GSM8864266,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells late HSPCs 6 dpf,For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions at 28C,cell type:Hematopoietic & Immune Cells,GSM8864266,GSM8864266: mCherry cells late HSPCs 6 dpf; Danio rerio; RNA Seq,GSM8864266 r1,GSM8864266,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options: readTypes=TBTT read1PairFiles=lateHSPC trace at 6dpf S17 L002 R1 001.fastq.gz read2PairFiles=lateHSPC trace at 6dpf S17 L002 R2 001.fastq.gz read3PairFiles=lateHSPC trace at 6dpf S17 L002 I1 001.fastq.gz read4PairFiles=lateHSPC trace at 6dpf S17 L002 I2 001.fastq.gz,lateHSPC_trace_at_6dpf_S17_L002_I1_001.fastq.gz lateHSPC_trace_at_6dpf_S17_L002_I2_001.fastq.gz lateHSPC_trace_at_6dpf_S17_L002_R1_001.fastq.gz lateHSPC_trace_at_6dpf_S17_L002_R2_001.fastq.gz,fastq fastq fastq fastq,12871712088.0,93273276.0,GSM8864266 r1,0:28 1:90 2:10 3:10,A:2421583617;C:1888963122;G:2078815965;T:2004213972;N:1018164,28,90,10,10,2421583617,1888963122,2078815965,2004213972,1018164,SRX28117238,SRS24473019,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System 35494,SRR32834040,SRX28117237,SRS24473014,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells late HSPCs 4 dpf,GSM8864265,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells late HSPCs 4 dpf,For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions at 28C,cell type:Hematopoietic & Immune Cells,GSM8864265,GSM8864265: mCherry cells late HSPCs 4 dpf; Danio rerio; RNA Seq,GSM8864265 r1,GSM8864265,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options: readTypes=TBTT read1PairFiles=lateHSPC trace at 4dpf S16 L002 R1 001.fastq.gz read2PairFiles=lateHSPC trace at 4dpf S16 L002 R2 001.fastq.gz read3PairFiles=lateHSPC trace at 4dpf S16 L002 I1 001.fastq.gz read4PairFiles=lateHSPC trace at 4dpf S16 L002 I2 001.fastq.gz,lateHSPC_trace_at_4dpf_S16_L002_I1_001.fastq.gz lateHSPC_trace_at_4dpf_S16_L002_I2_001.fastq.gz lateHSPC_trace_at_4dpf_S16_L002_R1_001.fastq.gz lateHSPC_trace_at_4dpf_S16_L002_R2_001.fastq.gz,fastq fastq fastq fastq,11138275734.0,80712143.0,GSM8864265 r1,0:28 1:90 2:10 3:10,A:2022661838;C:1679042427;G:1720706851;T:1840857883;N:823871,28,90,10,10,2022661838,1679042427,1720706851,1840857883,823871,SRX28117237,SRS24473014,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System 35495,SRR32834041,SRX28117236,SRS24473016,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells mid HSPCs 10 dpf,GSM8864264,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells mid HSPCs 10 dpf,For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions at 28C,cell type:Hematopoietic & Immune Cells,GSM8864264,GSM8864264: mCherry cells mid HSPCs 10 dpf; Danio rerio; RNA Seq,GSM8864264 r1,GSM8864264,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options: readTypes=TBTT read1PairFiles=midHSPC 10dpf S1 L001 R1 001.fastq.gz read2PairFiles=midHSPC 10dpf S1 L001 R2 001.fastq.gz read3PairFiles=midHSPC 10dpf S1 L001 I1 001.fastq.gz read4PairFiles=midHSPC 10dpf S1 L001 I2 001.fastq.gz,midHSPC_10dpf_S1_L001_I1_001.fastq.gz midHSPC_10dpf_S1_L001_I2_001.fastq.gz midHSPC_10dpf_S1_L001_R1_001.fastq.gz midHSPC_10dpf_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,211217834240.0,660055732.0,GSM8864264 r1,0:150 1:150 2:10 3:10,A:28426769480;C:22300370613;G:24520861829;T:23758933345;N:1424533,150,150,10,10,28426769480,22300370613,24520861829,23758933345,1424533,SRX28117236,SRS24473016,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System 35496,SRR32834042,SRX28117235,SRS24473020,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells mid HSPCs 6 dpf,GSM8864263,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells mid HSPCs 6 dpf,For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions at 28C,cell type:Hematopoietic & Immune Cells,GSM8864263,GSM8864263: mCherry cells mid HSPCs 6 dpf; Danio rerio; RNA Seq,GSM8864263 r1,GSM8864263,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options: readTypes=TBTT read1PairFiles=midHSPC 6dpf S1 L001 R1 001.fastq.gz read2PairFiles=midHSPC 6dpf S1 L001 R2 001.fastq.gz read3PairFiles=midHSPC 6dpf S1 L001 I1 001.fastq.gz read4PairFiles=midHSPC 6dpf S1 L001 I2 001.fastq.gz,midHSPC_6dpf_S1_L001_I1_001.fastq.gz midHSPC_6dpf_S1_L001_I2_001.fastq.gz midHSPC_6dpf_S1_L001_R1_001.fastq.gz midHSPC_6dpf_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,241173414720.0,753666921.0,GSM8864263 r1,,,,,,,,,,,,SRX28117235,SRS24473020,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,1,0.94667,,0.08748,,0.83881,,0.5015,,150,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System 35497,SRR32834043,SRX28117234,SRS24473021,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells mid HSPCs 3 dpf,GSM8864262,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells mid HSPCs 3 dpf,For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions at 28C,cell type:Hematopoietic & Immune Cells,GSM8864262,GSM8864262: mCherry cells mid HSPCs 3 dpf; Danio rerio; RNA Seq,GSM8864262 r1,GSM8864262,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options: readTypes=TBTT read1PairFiles=midHSPC 3dpf S6 L003 R1 001.fastq.gz read2PairFiles=midHSPC 3dpf S6 L003 R2 001.fastq.gz read3PairFiles=midHSPC 3dpf S6 L003 I1 001.fastq.gz read4PairFiles=midHSPC 3dpf S6 L003 I2 001.fastq.gz,midHSPC_3dpf_S6_L003_I1_001.fastq.gz midHSPC_3dpf_S6_L003_I2_001.fastq.gz midHSPC_3dpf_S6_L003_R1_001.fastq.gz midHSPC_3dpf_S6_L003_R2_001.fastq.gz,fastq fastq fastq fastq,71933359680.0,224791749.0,GSM8864262 r1,0:150 1:150 2:10 3:10,A:9519625855;C:6982221178;G:8366028895;T:7767873072;N:1083013350,150,150,10,10,9519625855,6982221178,8366028895,7767873072,1083013350,SRX28117234,SRS24473021,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,1,0.78368,,0.08584,,0.82144,,0.50936,,150,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System 35498,SRR32834044,SRX28117233,SRS24473012,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells early HSPCs 10 dpf,GSM8864261,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells early HSPCs 10 dpf,For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions at 28C,cell type:Hematopoietic & Immune Cells,GSM8864261,GSM8864261: mCherry cells early HSPCs 10 dpf; Danio rerio; RNA Seq,GSM8864261 r1,GSM8864261,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options: readTypes=TBTT read1PairFiles=earlyHSPC 10dpf S1 L001 R1 001.fastq.gz read2PairFiles=earlyHSPC 10dpf S1 L001 R2 001.fastq.gz read3PairFiles=earlyHSPC 10dpf S1 L001 I1 001.fastq.gz read4PairFiles=earlyHSPC 10dpf S1 L001 I2 001.fastq.gz,earlyHSPC_10dpf_S1_L001_I1_001.fastq.gz earlyHSPC_10dpf_S1_L001_I2_001.fastq.gz earlyHSPC_10dpf_S1_L001_R1_001.fastq.gz earlyHSPC_10dpf_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,267665197120.0,836453741.0,GSM8864261 r1,,,,,,,,,,,,SRX28117233,SRS24473012,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System 35499,SRR32834045,SRX28117232,SRS24473013,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells early HSPCs 6 dpf,GSM8864260,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells early HSPCs 6 dpf,For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions at 28C,cell type:Hematopoietic & Immune Cells,GSM8864260,GSM8864260: mCherry cells early HSPCs 6 dpf; Danio rerio; RNA Seq,GSM8864260 r1,GSM8864260,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options: readTypes=TBTT read1PairFiles=earlyHSPC 6dpf S1 L001 R1 001.fastq.gz read2PairFiles=earlyHSPC 6dpf S1 L001 R2 001.fastq.gz read3PairFiles=earlyHSPC 6dpf S1 L001 I1 001.fastq.gz read4PairFiles=earlyHSPC 6dpf S1 L001 I2 001.fastq.gz,earlyHSPC_6dpf_S1_L001_I1_001.fastq.gz earlyHSPC_6dpf_S1_L001_I2_001.fastq.gz earlyHSPC_6dpf_S1_L001_R1_001.fastq.gz earlyHSPC_6dpf_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,234759123200.0,733622260.0,GSM8864260 r1,,,,,,,,,,,,SRX28117232,SRS24473013,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System 35500,SRR32834046,SRX28117231,SRS24473011,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells early HSPCs 2 dpf,GSM8864259,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells early HSPCs 2 dpf,For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions at 28C,cell type:Hematopoietic & Immune Cells,GSM8864259,GSM8864259: mCherry cells early HSPCs 2 dpf; Danio rerio; RNA Seq,GSM8864259 r1,GSM8864259,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options: readTypes=TBTT read1PairFiles=earlyHSPC 2dpf S5 L003 R1 001.fastq.gz read2PairFiles=earlyHSPC 2dpf S5 L003 R2 001.fastq.gz read3PairFiles=earlyHSPC 2dpf S5 L003 I1 001.fastq.gz read4PairFiles=earlyHSPC 2dpf S5 L003 I2 001.fastq.gz,earlyHSPC_2dpf_S5_L003_I1_001.fastq.gz earlyHSPC_2dpf_S5_L003_I2_001.fastq.gz earlyHSPC_2dpf_S5_L003_R1_001.fastq.gz earlyHSPC_2dpf_S5_L003_R2_001.fastq.gz,fastq fastq fastq fastq,80730897280.0,252284054.0,GSM8864259 r1,0:150 1:150 2:10 3:10,A:10564796609;C:7860706889;G:9394625294;T:8808848403;N:1213630905,150,150,10,10,10564796609,7860706889,9394625294,8808848403,1213630905,SRX28117231,SRS24473011,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Multi-stage,Multi-stage,Blood,Hematopoietic 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.,,pubmed:40501392,,5 dpf hematopoietic zebrafish cells session 2,GSM9052756,,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,,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°C 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 µg/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°C 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 µl FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 μm 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 µl 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 ß actin DNA quality control using a TapeStation Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.,,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°C 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 µg/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°C 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 µl FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 μm 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 µl 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 ß actin DNA quality control using a TapeStation Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP592701,,,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,,,2003237489,1403878506,1540717140,1805684398,2369733604,SRX29213468,SRS25409913,SRA2151098,Institut Pasteur,Institut Pasteur,,,,,,,,,,,,,,,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,marsseq,,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.,,pubmed:40501392,,5 dpf hematopoietic zebrafish cells session 2,GSM9052756,,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,,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°C 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 µg/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°C 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 µl FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 μm 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 µl 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 ß actin DNA quality control using a TapeStation Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.,,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°C 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 µg/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°C 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 µl FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 μm 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 µl 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 ß actin DNA quality control using a TapeStation Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP592701,,,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,,,2023532922,1427491871,1568162363,1827659977,2402443995,SRX29213468,SRS25409913,SRA2151098,Institut Pasteur,Institut Pasteur,,,,,,,,,,,,,,,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,marsseq,,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.,,pubmed:40501392,,5 dpf hematopoietic zebrafish cells session 2,GSM9052756,,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,,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°C 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 µg/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°C 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 µl FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 μm 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 µl 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 ß actin DNA quality control using a TapeStation Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.,,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°C 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 µg/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°C 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 µl FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 μm 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 µl 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 ß actin DNA quality control using a TapeStation Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP592701,,,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,,,2061159862,1455510691,1599304279,1871072315,2451648427,SRX29213468,SRS25409913,SRA2151098,Institut Pasteur,Institut Pasteur,,,,,,,,,,,,,,,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,marsseq,,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.,,pubmed:40501392,,5 dpf hematopoietic zebrafish cells session 2,GSM9052756,,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,,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°C 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 µg/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°C 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 µl FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 μm 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 µl 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 ß actin DNA quality control using a TapeStation Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.,,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°C 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 µg/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°C 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 µl FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 μm 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 µl 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 ß actin DNA quality control using a TapeStation Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP592701,,,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,,,2048111796,1451606983,1595602008,1870010070,2444016013,SRX29213468,SRS25409913,SRA2151098,Institut Pasteur,Institut Pasteur,,,,,,,,,,,,,,,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,marsseq,,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.,,pubmed:40501392,,5 dpf hematopoietic zebrafish cells session 1,GSM9052755,,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,,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°C 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 µg/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°C 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 µl FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 μm 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 µl 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 ß actin DNA quality control using a TapeStation Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.,,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°C 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 µg/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°C 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 µl FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 μm 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 µl 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 ß actin DNA quality control using a TapeStation Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP592701,,,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,,,12324583812,8979463244,11486707902,13012728622,13584580,SRX29213467,SRS25409912,SRA2151098,Institut Pasteur,Institut Pasteur,,,,,,,,,,,,B,T,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,marsseq,,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.,,pubmed:40501392,,5 dpf hematopoietic zebrafish cells session 1,GSM9052755,,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,,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°C 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 µg/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°C 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 µl FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 μm 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 µl 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 ß actin DNA quality control using a TapeStation Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.,,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°C 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 µg/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°C 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 µl FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 μm 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 µl 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 ß actin DNA quality control using a TapeStation Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP592701,,,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,,,50399,36081,47775,53618,2127,SRX29213467,SRS25409912,SRA2151098,Institut Pasteur,Institut Pasteur,,,,,,,,,,,,B,T,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,marsseq,,France,2025-06-17,Larval,Larval,Blood,Hematopoietic System 70833,SRR20668414,SRX16690958,SRS14321723,SRP388388,PRJNA862882,An anti inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish,GSE209884,Transcriptome Analysis,Single cell RNA sequencing on FACS sorted cells from the zebrafish macrophage in 5df embryos in 11 different samples: homeo 15min neomycin 1hr post neo 3hr post neo 5hr post neo il10ra sib homeo il10ra sib 1hr il10ra sib 3hr il10ra mut homeo il10ra mut 1hr and il10ra mut 3hr Overall design: scRNA seq,,pubmed:36127326,,3hr il10ra mut homozygous/mutant,GSM6404047,,source name:macrophage|age:5dpf|tissue:macrophage|genotype:3hr il10ra mut homozygous/mutant|strain:Tgmpeg:GFP,3hr il10ra mut homozygous/mutant,Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 ensembl release 91 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Assembly: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.,macrophage,,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,age:5dpf|tissue:macrophage|genotype:3hr il10ra mut homozygous/mutant|strain:Tgmpeg:GFP,GSM6404047,GSM6404047: 3hr il10ra mut homozygous/mutant; Danio rerio; RNA Seq,GSM6404047 r1,GSM6404047,1,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP388388,,intentional duplicate|dangling references:treat as unmapped,3h_il10ra_mut_possorted_genome_bam.bam,10X Genomics bam file,62119485701.0,682631711.0,GSM6404047 r1,0:91,A:19063458673;C:12969646294;G:14996142121;T:15088275965;N:1962648,91,,,,19063458673,12969646294,14996142121,15088275965,1962648,SRX16690958,SRS14321723,SRA1469295,Stowers institute for medical research,Stowers institute for medical research,1,0.90083,,0.13953,,0.81852,,0.58114,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-07-27,Larval,Larval,Blood,Hematopoietic System 70834,SRR20668415,SRX16690957,SRS14321722,SRP388388,PRJNA862882,An anti inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish,GSE209884,Transcriptome Analysis,Single cell RNA sequencing on FACS sorted cells from the zebrafish macrophage in 5df embryos in 11 different samples: homeo 15min neomycin 1hr post neo 3hr post neo 5hr post neo il10ra sib homeo il10ra sib 1hr il10ra sib 3hr il10ra mut homeo il10ra mut 1hr and il10ra mut 3hr Overall design: scRNA seq,,pubmed:36127326,,1hr il10ra mut homozygous/mutant,GSM6404046,,source name:macrophage|age:5dpf|tissue:macrophage|genotype:1hr il10ra mut homozygous/mutant|strain:Tgmpeg:GFP,1hr il10ra mut homozygous/mutant,Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 ensembl release 91 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Assembly: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.,macrophage,,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,age:5dpf|tissue:macrophage|genotype:1hr il10ra mut homozygous/mutant|strain:Tgmpeg:GFP,GSM6404046,GSM6404046: 1hr il10ra mut homozygous/mutant; Danio rerio; RNA Seq,GSM6404046 r1,GSM6404046,1,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP388388,,intentional duplicate|dangling references:treat as unmapped,1h_il10ra_mut_possorted_genome_bam.bam,10X Genomics bam file,53760457023.0,590774253.0,GSM6404046 r1,0:91,A:16112436932;C:11497272850;G:13478420835;T:12670631386;N:1695020,91,,,,16112436932,11497272850,13478420835,12670631386,1695020,SRX16690957,SRS14321722,SRA1469295,Stowers institute for medical research,Stowers institute for medical research,1,0.88181,,0.15256,,0.84642,,0.59854,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-07-27,Larval,Larval,Blood,Hematopoietic System 70835,SRR20668416,SRX16690956,SRS14321721,SRP388388,PRJNA862882,An anti inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish,GSE209884,Transcriptome Analysis,Single cell RNA sequencing on FACS sorted cells from the zebrafish macrophage in 5df embryos in 11 different samples: homeo 15min neomycin 1hr post neo 3hr post neo 5hr post neo il10ra sib homeo il10ra sib 1hr il10ra sib 3hr il10ra mut homeo il10ra mut 1hr and il10ra mut 3hr Overall design: scRNA seq,,pubmed:36127326,,homeo il10ra mut homozygous/mutant,GSM6404045,,source name:macrophage|age:5dpf|tissue:macrophage|genotype:homeo il10ra mut homozygous/mutant|strain:Tgmpeg:GFP,homeo il10ra mut homozygous/mutant,Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 ensembl release 91 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Assembly: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.,macrophage,,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,age:5dpf|tissue:macrophage|genotype:homeo il10ra mut homozygous/mutant|strain:Tgmpeg:GFP,GSM6404045,GSM6404045: homeo il10ra mut homozygous/mutant; Danio rerio; RNA Seq,GSM6404045 r1,GSM6404045,1,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP388388,,intentional duplicate|dangling references:treat as unmapped,homeo_il10ra_mut_possorted_genome_bam.bam,10X Genomics bam file,54884218571.0,603123281.0,GSM6404045 r1,0:91,A:16107511497;C:11798904382;G:12911246344;T:14064824012;N:1732336,91,,,,16107511497,11798904382,12911246344,14064824012,1732336,SRX16690956,SRS14321721,SRA1469295,Stowers institute for medical research,Stowers institute for medical research,1,0.92347,,0.15847,,0.80762,,0.4962,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-07-27,Larval,Larval,Blood,Hematopoietic System 70836,SRR20668417,SRX16690955,SRS14321720,SRP388388,PRJNA862882,An anti inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish,GSE209884,Transcriptome Analysis,Single cell RNA sequencing on FACS sorted cells from the zebrafish macrophage in 5df embryos in 11 different samples: homeo 15min neomycin 1hr post neo 3hr post neo 5hr post neo il10ra sib homeo il10ra sib 1hr il10ra sib 3hr il10ra mut homeo il10ra mut 1hr and il10ra mut 3hr Overall design: scRNA seq,,pubmed:36127326,,3hr il10ra sib heterozygous/sibling,GSM6404044,,source name:macrophage|age:5dpf|tissue:macrophage|genotype:3hr il10ra sib heterozygous/sibling|strain:Tgmpeg:GFP,3hr il10ra sib heterozygous/sibling,Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 ensembl release 91 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Assembly: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.,macrophage,,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,age:5dpf|tissue:macrophage|genotype:3hr il10ra sib heterozygous/sibling|strain:Tgmpeg:GFP,GSM6404044,GSM6404044: 3hr il10ra sib heterozygous/sibling; Danio rerio; RNA Seq,GSM6404044 r1,GSM6404044,1,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP388388,,intentional duplicate|dangling references:treat as unmapped,3h_il10ra_sib_possorted_genome_bam.bam,10X Genomics bam file,76164218312.0,836969432.0,GSM6404044 r1,0:91,A:24495666579;C:15379395913;G:18054974511;T:18231782170;N:2399139,91,,,,24495666579,15379395913,18054974511,18231782170,2399139,SRX16690955,SRS14321720,SRA1469295,Stowers institute for medical research,Stowers institute for medical research,1,0.8984,,0.13627,,0.8254,,0.5844,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-07-27,Larval,Larval,Blood,Hematopoietic System 70837,SRR20668418,SRX16690954,SRS14321718,SRP388388,PRJNA862882,An anti inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish,GSE209884,Transcriptome Analysis,Single cell RNA sequencing on FACS sorted cells from the zebrafish macrophage in 5df embryos in 11 different samples: homeo 15min neomycin 1hr post neo 3hr post neo 5hr post neo il10ra sib homeo il10ra sib 1hr il10ra sib 3hr il10ra mut homeo il10ra mut 1hr and il10ra mut 3hr Overall design: scRNA seq,,pubmed:36127326,,1hr il10ra sib heterozygous/sibling,GSM6404043,,source name:macrophage|age:5dpf|tissue:macrophage|genotype:1hr il10ra sib heterozygous/sibling|strain:Tgmpeg:GFP,1hr il10ra sib heterozygous/sibling,Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 ensembl release 91 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Assembly: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.,macrophage,,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,age:5dpf|tissue:macrophage|genotype:1hr il10ra sib heterozygous/sibling|strain:Tgmpeg:GFP,GSM6404043,GSM6404043: 1hr il10ra sib heterozygous/sibling; Danio rerio; RNA Seq,GSM6404043 r1,GSM6404043,1,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP388388,,intentional duplicate|dangling references:treat as unmapped,1h_il10ra_sib_possorted_genome_bam.bam,10X Genomics bam file,55980175069.0,615166759.0,GSM6404043 r1,0:91,A:17214450499;C:11610450029;G:13903261037;T:13250244220;N:1769284,91,,,,17214450499,11610450029,13903261037,13250244220,1769284,SRX16690954,SRS14321718,SRA1469295,Stowers institute for medical research,Stowers institute for medical research,1,0.86967,,0.1721,,0.84147,,0.6182,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-07-27,Larval,Larval,Blood,Hematopoietic System 70838,SRR20668419,SRX16690953,SRS14321719,SRP388388,PRJNA862882,An anti inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish,GSE209884,Transcriptome Analysis,Single cell RNA sequencing on FACS sorted cells from the zebrafish macrophage in 5df embryos in 11 different samples: homeo 15min neomycin 1hr post neo 3hr post neo 5hr post neo il10ra sib homeo il10ra sib 1hr il10ra sib 3hr il10ra mut homeo il10ra mut 1hr and il10ra mut 3hr Overall design: scRNA seq,,pubmed:36127326,,homeo il10ra sib heterozygous/sibling,GSM6404042,,source name:macrophage|age:5dpf|tissue:macrophage|genotype:homeo il10ra sib heterozygous/sibling|strain:Tgmpeg:GFP,homeo il10ra sib heterozygous/sibling,Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 ensembl release 91 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Assembly: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.,macrophage,,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,age:5dpf|tissue:macrophage|genotype:homeo il10ra sib heterozygous/sibling|strain:Tgmpeg:GFP,GSM6404042,GSM6404042: homeo il10ra sib heterozygous/sibling; Danio rerio; RNA Seq,GSM6404042 r1,GSM6404042,1,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP388388,,intentional duplicate|dangling references:treat as unmapped,homeo_il10ra_sib_possorted_genome_bam.bam,10X Genomics bam file,65823260594.0,723332534.0,GSM6404042 r1,0:91,A:19277950772;C:14136710715;G:15444723963;T:16961801916;N:2073228,91,,,,19277950772,14136710715,15444723963,16961801916,2073228,SRX16690953,SRS14321719,SRA1469295,Stowers institute for medical research,Stowers institute for medical research,1,0.92472,,0.14491,,0.8103,,0.56302,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-07-27,Larval,Larval,Blood,Hematopoietic System 70839,SRR20668420,SRX16690952,SRS14321717,SRP388388,PRJNA862882,An anti inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish,GSE209884,Transcriptome Analysis,Single cell RNA sequencing on FACS sorted cells from the zebrafish macrophage in 5df embryos in 11 different samples: homeo 15min neomycin 1hr post neo 3hr post neo 5hr post neo il10ra sib homeo il10ra sib 1hr il10ra sib 3hr il10ra mut homeo il10ra mut 1hr and il10ra mut 3hr Overall design: scRNA seq,,pubmed:36127326,,5hr post neomycin,GSM6404041,,source name:macrophage|age:5dpf|tissue:macrophage|genotype:5hr post neomycin|strain:Tgmpeg:GFP,5hr post neomycin,Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 ensembl release 91 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Assembly: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.,macrophage,,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,age:5dpf|tissue:macrophage|genotype:5hr post neomycin|strain:Tgmpeg:GFP,GSM6404041,GSM6404041: 5hr post neomycin; Danio rerio; RNA Seq,GSM6404041 r1,GSM6404041,1,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP388388,,assembly:danRer10|intentional duplicate|dangling references:treat as unmapped,5hr_possorted_genome_bam.bam,10X Genomics bam file,35604069046.0,391253506.0,GSM6404041 r1,0:91,A:10384029234;C:7578909209;G:8255823659;T:9384782607;N:524337,91,,,,10384029234,7578909209,8255823659,9384782607,524337,SRX16690952,SRS14321717,SRA1469295,Stowers institute for medical research,Stowers institute for medical research,1,0.93723,,0.11988,,0.80541,,0.54155,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-07-27,Larval,Larval,Blood,Hematopoietic System 70840,SRR20668421,SRX16690951,SRS14321716,SRP388388,PRJNA862882,An anti inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish,GSE209884,Transcriptome Analysis,Single cell RNA sequencing on FACS sorted cells from the zebrafish macrophage in 5df embryos in 11 different samples: homeo 15min neomycin 1hr post neo 3hr post neo 5hr post neo il10ra sib homeo il10ra sib 1hr il10ra sib 3hr il10ra mut homeo il10ra mut 1hr and il10ra mut 3hr Overall design: scRNA seq,,pubmed:36127326,,3hr post neomycin,GSM6404040,,source name:macrophage|age:5dpf|tissue:macrophage|genotype:3hr post neomycin|strain:Tgmpeg:GFP,3hr post neomycin,Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 ensembl release 91 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Assembly: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.,macrophage,,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,age:5dpf|tissue:macrophage|genotype:3hr post neomycin|strain:Tgmpeg:GFP,GSM6404040,GSM6404040: 3hr post neomycin; Danio rerio; RNA Seq,GSM6404040 r1,GSM6404040,1,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP388388,,assembly:danRer10|intentional duplicate|dangling references:treat as unmapped,3h_possorted_genome_bam.bam,10X Genomics bam file,33149245584.0,364277424.0,GSM6404040 r1,0:91,A:9699362543;C:7042480303;G:7729260559;T:8677650345;N:491834,91,,,,9699362543,7042480303,7729260559,8677650345,491834,SRX16690951,SRS14321716,SRA1469295,Stowers institute for medical research,Stowers institute for medical research,1,0.93611,,0.12582,,0.80476,,0.53981,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-07-27,Larval,Larval,Blood,Hematopoietic System 70841,SRR20668422,SRX16690950,SRS14321715,SRP388388,PRJNA862882,An anti inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish,GSE209884,Transcriptome Analysis,Single cell RNA sequencing on FACS sorted cells from the zebrafish macrophage in 5df embryos in 11 different samples: homeo 15min neomycin 1hr post neo 3hr post neo 5hr post neo il10ra sib homeo il10ra sib 1hr il10ra sib 3hr il10ra mut homeo il10ra mut 1hr and il10ra mut 3hr Overall design: scRNA seq,,pubmed:36127326,,1hr post neomycin,GSM6404039,,source name:macrophage|age:5dpf|tissue:macrophage|genotype:1hr post neomycin|strain:Tgmpeg:GFP,1hr post neomycin,Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 ensembl release 91 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Assembly: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.,macrophage,,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,age:5dpf|tissue:macrophage|genotype:1hr post neomycin|strain:Tgmpeg:GFP,GSM6404039,GSM6404039: 1hr post neomycin; Danio rerio; RNA Seq,GSM6404039 r1,GSM6404039,1,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP388388,,assembly:danRer10|intentional duplicate|dangling references:treat as unmapped,1hr_possorted_genome_bam.bam,10X Genomics bam file,31569863871.0,346921581.0,GSM6404039 r1,0:91,A:9269126254;C:6667515682;G:7316895497;T:8315860639;N:465799,91,,,,9269126254,6667515682,7316895497,8315860639,465799,SRX16690950,SRS14321715,SRA1469295,Stowers institute for medical research,Stowers institute for medical research,1,0.93105,,0.12507,,0.81677,,0.52209,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-07-27,Larval,Larval,Blood,Hematopoietic System 70842,SRR20668423,SRX16690949,SRS14321714,SRP388388,PRJNA862882,An anti inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish,GSE209884,Transcriptome Analysis,Single cell RNA sequencing on FACS sorted cells from the zebrafish macrophage in 5df embryos in 11 different samples: homeo 15min neomycin 1hr post neo 3hr post neo 5hr post neo il10ra sib homeo il10ra sib 1hr il10ra sib 3hr il10ra mut homeo il10ra mut 1hr and il10ra mut 3hr Overall design: scRNA seq,,pubmed:36127326,,15min post neomycin,GSM6404038,,source name:macrophage|age:5dpf|tissue:macrophage|genotype:15min post neomycin|strain:Tgmpeg:GFP,15min post neomycin,Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 ensembl release 91 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Assembly: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.,macrophage,,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,age:5dpf|tissue:macrophage|genotype:15min post neomycin|strain:Tgmpeg:GFP,GSM6404038,GSM6404038: 15min post neomycin; Danio rerio; RNA Seq,GSM6404038 r1,GSM6404038,1,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP388388,,assembly:danRer10|intentional duplicate,15min_possorted_genome_bam.bam,10X Genomics bam file,31511277963.0,318295737.0,GSM6404038 r1,0:99,A:9298906016;C:6733626243;G:7314474144;T:8157192656;N:7078904,99,,,,9298906016,6733626243,7314474144,8157192656,7078904,SRX16690949,SRS14321714,SRA1469295,Stowers institute for medical research,Stowers institute for medical research,1,0.92846,,0.11694,,0.82055,,0.52675,,99,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-07-27,Larval,Larval,Blood,Hematopoietic System 70843,SRR20668424,SRX16690948,SRS14321713,SRP388388,PRJNA862882,An anti inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish,GSE209884,Transcriptome Analysis,Single cell RNA sequencing on FACS sorted cells from the zebrafish macrophage in 5df embryos in 11 different samples: homeo 15min neomycin 1hr post neo 3hr post neo 5hr post neo il10ra sib homeo il10ra sib 1hr il10ra sib 3hr il10ra mut homeo il10ra mut 1hr and il10ra mut 3hr Overall design: scRNA seq,,pubmed:36127326,,homeo,GSM6404037,,source name:macrophage|age:5dpf|tissue:macrophage|genotype:homeo|strain:Tgmpeg:GFP,homeo,Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10 ensembl release 91 using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Assembly: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.,macrophage,,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,age:5dpf|tissue:macrophage|genotype:homeo|strain:Tgmpeg:GFP,GSM6404037,GSM6404037: homeo; Danio rerio; RNA Seq,GSM6404037 r1,GSM6404037,1,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP388388,,assembly:danRer10|intentional duplicate,homeo_possorted_genome_bam.bam,10X Genomics bam file,14120576910.0,142632090.0,GSM6404037 r1,0:99,A:4214242258;C:2942873461;G:3198194603;T:3761817001;N:3449587,99,,,,4214242258,2942873461,3198194603,3761817001,3449587,SRX16690948,SRS14321713,SRA1469295,Stowers institute for medical research,Stowers institute for medical research,1,0.91899,,0.15518,,0.81659,,0.54276,,99,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-07-27,Larval,Larval,Blood,Hematopoietic System