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45 rows where experiment.library_selection = "cDNA", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and tissue_curation = "Blood"

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tissue_curation 1

  • Blood · 45 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

  • TRANSCRIPTOMIC SINGLE CELL · 45 ✖

experiment.library_selection 1

  • cDNA · 45 ✖

experiment.library_layout 1

Link 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
29175 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 de…   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 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 de…   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 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 de…   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 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 de…   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 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 de…   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 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 de…   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 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 de…   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 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 de…   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 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 de…   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 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 de…   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 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 de…   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 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 de…   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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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…   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 …   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 …   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 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…   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 …   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 …   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 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…   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 …   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 …   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 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…   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 …   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 …   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 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…   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 …   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 …   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 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…   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 …   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 …   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 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 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 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 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 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 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 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 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 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 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 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

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