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,SRR27292304,SRX22969963,SRS19936063,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Burned Larval Zebrafish  48 hours post burn,GSM7982886,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing,Burned Larval Zebrafish  48 hours post burn,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn,GSM7982886,GSM7982886: Burned Larval Zebrafish  48 hours post burn; Danio rerio; RNA Seq,GSM7982886 r1,GSM7982886,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,Burn-48hpb_S5_L001_R2_001.fastq.gz Burn-48hpb_S5_L001_R1_001.fastq.gz,fastq fastq,20874980529.0,178418637.0,GSM7982886 r1,0:28 1:89,A:5945091269;C:4392590896;G:4497688824;T:6035946283;N:3663257,28,89,,,5945091269,4392590896,4497688824,6035946283,3663257,SRX22969963,SRS19936063,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.00573,0.91666,0.00222,0.19474,0.9931,0.79306,0.42082,0.53801,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System
29176,SRR27292305,SRX22969963,SRS19936063,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Burned Larval Zebrafish  48 hours post burn,GSM7982886,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing,Burned Larval Zebrafish  48 hours post burn,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn,GSM7982886,GSM7982886: Burned Larval Zebrafish  48 hours post burn; Danio rerio; RNA Seq,GSM7982886 r1,GSM7982886,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,Burn-48hpb_S5_L002_R1_001.fastq.gz Burn-48hpb_S5_L002_R2_001.fastq.gz,fastq fastq,20022973425.0,171136525.0,GSM7982886 r2,0:28 1:89,A:5709681181;C:4208386174;G:4307510275;T:5796282368;N:1113427,28,89,,,5709681181,4208386174,4307510275,5796282368,1113427,SRX22969963,SRS19936063,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.00547,0.9154,0.00202,0.1955,0.99283,0.79423,0.39307,0.53427,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System
29177,SRR27292306,SRX22969962,SRS19936064,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Burned Larval Zebrafish  24 hours post burn,GSM7982885,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing,Burned Larval Zebrafish  24 hours post burn,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn,GSM7982885,GSM7982885: Burned Larval Zebrafish  24 hours post burn; Danio rerio; RNA Seq,GSM7982885 r1,GSM7982885,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,Burn-24hpb_S2_L001_R1_001.fastq.gz Burn-24hpb_S2_L001_R2_001.fastq.gz,fastq fastq,9782870058.0,83614274.0,GSM7982885 r1,0:28 1:89,A:2744737668;C:2140848416;G:2249400157;T:2645170677;N:2713140,28,89,,,2744737668,2140848416,2249400157,2645170677,2713140,SRX22969962,SRS19936064,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.00752,0.92059,0.00244,0.16143,0.98944,0.82929,0.44176,0.54525,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System
29178,SRR27292307,SRX22969962,SRS19936064,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Burned Larval Zebrafish  24 hours post burn,GSM7982885,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing,Burned Larval Zebrafish  24 hours post burn,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn,GSM7982885,GSM7982885: Burned Larval Zebrafish  24 hours post burn; Danio rerio; RNA Seq,GSM7982885 r1,GSM7982885,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,Burn-24hpb_S2_L002_R2_001.fastq.gz Burn-24hpb_S2_L002_R1_001.fastq.gz,fastq fastq,9861989202.0,84290506.0,GSM7982885 r2,0:28 1:89,A:2769268861;C:2158644227;G:2263475493;T:2669311436;N:1289185,28,89,,,2769268861,2158644227,2263475493,2669311436,1289185,SRX22969962,SRS19936064,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.0076,0.9197,0.00232,0.16162,0.98995,0.82852,0.43786,0.55256,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System
29179,SRR27292308,SRX22969961,SRS19936062,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Burned Larval Zebrafish  6 hours post burn,GSM7982884,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing,Burned Larval Zebrafish  6 hours post burn,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn,GSM7982884,GSM7982884: Burned Larval Zebrafish  6 hours post burn; Danio rerio; RNA Seq,GSM7982884 r1,GSM7982884,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,Burn-6hpb_S7_L001_R1_001.fastq.gz Burn-6hpb_S7_L001_R2_001.fastq.gz,fastq fastq,12475938384.0,106631952.0,GSM7982884 r1,0:28 1:89,A:3401989108;C:2878275107;G:3114945415;T:3078525361;N:2203393,28,89,,,3401989108,2878275107,3114945415,3078525361,2203393,SRX22969961,SRS19936062,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.01053,0.89396,0.00429,0.18315,0.99458,0.85756,0.34876,0.58728,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System
29180,SRR27292309,SRX22969961,SRS19936062,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Burned Larval Zebrafish  6 hours post burn,GSM7982884,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing,Burned Larval Zebrafish  6 hours post burn,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn,GSM7982884,GSM7982884: Burned Larval Zebrafish  6 hours post burn; Danio rerio; RNA Seq,GSM7982884 r1,GSM7982884,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,Burn-6hpb_S7_L002_R1_001.fastq.gz Burn-6hpb_S7_L002_R2_001.fastq.gz,fastq fastq,11874083247.0,101487891.0,GSM7982884 r2,0:28 1:89,A:3243501055;C:2735412615;G:2958387721;T:2936117380;N:664476,28,89,,,3243501055,2735412615,2958387721,2936117380,664476,SRX22969961,SRS19936062,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.01063,0.89389,0.00439,0.18047,0.99403,0.85878,0.36393,0.54831,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System
29181,SRR27292310,SRX22969960,SRS19936061,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Unwounded Larval Zebrafish  5 dpf,GSM7982883,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing,Unwounded Larval Zebrafish  5 dpf,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded,GSM7982883,GSM7982883: Unwounded Larval Zebrafish  5 dpf Danio rerio; RNA Seq,GSM7982883 r1,GSM7982883,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,WT-5dpf_S6_L001_R2_001.fastq.gz WT-5dpf_S6_L001_R1_001.fastq.gz,fastq fastq,31813158312.0,271907336.0,GSM7982883 r1,0:28 1:89,A:8991313503;C:6911976524;G:7105775004;T:8798521232;N:5572049,28,89,,,8991313503,6911976524,7105775004,8798521232,5572049,SRX22969960,SRS19936061,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.00661,0.92343,0.00245,0.19293,0.99255,0.81379,0.35935,0.54818,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System
29182,SRR27292311,SRX22969960,SRS19936061,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Unwounded Larval Zebrafish  5 dpf,GSM7982883,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing,Unwounded Larval Zebrafish  5 dpf,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded,GSM7982883,GSM7982883: Unwounded Larval Zebrafish  5 dpf Danio rerio; RNA Seq,GSM7982883 r1,GSM7982883,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,WT-5dpf_S6_L002_R1_001.fastq.gz WT-5dpf_S6_L002_R2_001.fastq.gz,fastq fastq,30524386113.0,260892189.0,GSM7982883 r2,0:28 1:89,A:8637605077;C:6625244702;G:6807369409;T:8452468968;N:1697957,28,89,,,8637605077,6625244702,6807369409,8452468968,1697957,SRX22969960,SRS19936061,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.00648,0.92418,0.00233,0.19549,0.99241,0.81444,0.37733,0.54674,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System
29183,SRR27292312,SRX22969959,SRS19936060,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Unwounded Larval Zebrafish  4 dpf,GSM7982882,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing,Unwounded Larval Zebrafish  4 dpf,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded,GSM7982882,GSM7982882: Unwounded Larval Zebrafish  4 dpf Danio rerio; RNA Seq,GSM7982882 r1,GSM7982882,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,WT-4dpf_S1_L001_R1_001.fastq.gz WT-4dpf_S1_L001_R2_001.fastq.gz,fastq fastq,12682286721.0,108395613.0,GSM7982882 r1,0:28 1:89,A:3575375325;C:2777398557;G:2900088646;T:3425909511;N:3514682,28,89,,,3575375325,2777398557,2900088646,3425909511,3514682,SRX22969959,SRS19936060,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.00505,0.92112,0.00185,0.16865,0.99257,0.8258,0.38216,0.5512,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System
29184,SRR27292313,SRX22969959,SRS19936060,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Unwounded Larval Zebrafish  4 dpf,GSM7982882,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing,Unwounded Larval Zebrafish  4 dpf,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded,GSM7982882,GSM7982882: Unwounded Larval Zebrafish  4 dpf Danio rerio; RNA Seq,GSM7982882 r1,GSM7982882,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,WT-4dpf_S1_L002_R2_001.fastq.gz WT-4dpf_S1_L002_R1_001.fastq.gz,fastq fastq,12832453413.0,109679089.0,GSM7982882 r2,0:28 1:89,A:3620789787;C:2810897812;G:2929508681;T:3469577031;N:1680102,28,89,,,3620789787,2810897812,2929508681,3469577031,1680102,SRX22969959,SRS19936060,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.0052,0.92355,0.00192,0.16775,0.99263,0.8253,0.37089,0.55115,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System
29185,SRR27292314,SRX22969958,SRS19936059,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Unwounded Larval Zebrafish  3 dpf,GSM7982881,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing,Unwounded Larval Zebrafish  3 dpf,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded,GSM7982881,GSM7982881: Unwounded Larval Zebrafish  3 dpf Danio rerio; RNA Seq,GSM7982881 r1,GSM7982881,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,WT-3dpf_S4_L001_R1_001.fastq.gz WT-3dpf_S4_L001_R2_001.fastq.gz,fastq fastq,7586138430.0,64838790.0,GSM7982881 r1,0:28 1:89,A:2101749534;C:1692875352;G:1784872358;T:2005308370;N:1332816,28,89,,,2101749534,1692875352,1784872358,2005308370,1332816,SRX22969958,SRS19936059,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.00976,0.92096,0.00368,0.18077,0.99356,0.83875,0.3661,0.59073,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System
29186,SRR27292315,SRX22969958,SRS19936059,SRP479046,PRJNA1054617,Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish,GSE250610,Transcriptome Analysis,Neutrophils accumulate early in burn wounds  and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However  we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here  we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions  we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils  with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality  suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore  we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways  we found il6 il6r signaling as a time point specific macrophage neutrophil interaction  suggesting the importance of timing in innate immune response in burn. Finally  to test the translational value of our fish model  we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the degree of total body surface area TBSA in patients. Flow cytometry confirmed the presence of neutrophils carrying these signatures in patient's blood. Our findings demonstrate the potential of using zebrafish as a model to identify early innate immune response signatures that could inform a timely treatment of burn in humans. This work builds the molecular foundation and a comparative single cell genomic framework to guide future identification of actionable pathways to burn wound healing in patients. Overall design: At 6/24/48 hour post burn hpb  burned and unwounded larvae at matching developmental stages 3/4/5 dpf dpf were transferred to 35 mm dish containing calcium free PBS for 15 min and then anesthetized with tricaine methanesulfonate MS222  200 mg/L. A total of 150 fish were used for each time point by condition. Each dish of fish was digested with 2 mL digestion solution 0.25% trypsin  1mM EDTA in PBS at 28.5°C for 90 min with gentle pipetting every 10 min. Digestion was stopped by adding 200 mL digestion stop solution 1mM CaCl2  100% FBS. Dissociated cells were filtered with 40 mm cell strainers and centrifuged for 3 min at 3 000 rpm at 4 °C. Cell pellets were resuspended in PBS with 10% FBS plus DAPI 1mg/mL. Fluorescence activated cell sorting FACS was performed at University of Wisconsin Carbone Cancer Center Flow Lab using BD FACSAria. Targeted cells passed gating for cells versus debris  singles versus doublets  live versus dead and were high in either 488 nm/561 nm channel. Both dendra+ 488 nm channel and mCherry+ 561 nm channel cells were sorted into PBS with 10% FBS. Post sorting  cells were directly used for library construction in a Chromium controller at the Gene Expression Center of the University of Wisconsin Madison Biotechnology Center RRID: SCR 017757. Samples were processed with Chromium Single Cell Gene Expression Solution three prime v2 10X Genomics.,,pubmed:38922186,,Unwounded Larval Zebrafish  3 dpf,GSM7982881,,source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing,Unwounded Larval Zebrafish  3 dpf,FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days  Burn 24 hours  v6.1.2 Unwounded 3days  Unwounded 5days  Burn 6hours  Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix,Whole blood,Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.,tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded,GSM7982881,GSM7982881: Unwounded Larval Zebrafish  3 dpf Danio rerio; RNA Seq,GSM7982881 r1,GSM7982881,1,Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP479046,,loader:fastq load.py,WT-3dpf_S4_L002_R1_001.fastq.gz WT-3dpf_S4_L002_R2_001.fastq.gz,fastq fastq,7258692168.0,62040104.0,GSM7982881 r2,0:28 1:89,A:2013529524;C:1617959197;G:1704796898;T:1922004726;N:401823,28,89,,,2013529524,1617959197,1704796898,1922004726,401823,SRX22969958,SRS19936059,SRA1772557,University of Wisconsin-Madison,University of Wisconsin-Madison,2,0.00949,0.92207,0.00359,0.18081,0.99375,0.83751,0.37347,0.55889,28,89,T,B,sc-like readlen,illumina,novaseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2023-12-19,Multi-stage,Multi-stage,Blood,Hematopoietic System
35485,SRR32834031,SRX28117245,SRS24473023,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  rag1 crispant  R848 treated,GSM8864273,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|genotype:rag1 mosaic mutant|treatment:Resiquimod R848 treated|geo loc name:missing|collection date:missing,mCherry cells  rag1 crispant  R848 treated,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells|genotype:rag1 mosaic mutant|treatment:Resiquimod R848 treated,GSM8864273,GSM8864273: mCherry cells  rag1 crispant  R848 treated; Danio rerio; RNA Seq,GSM8864273 r1,GSM8864273,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=Rag1 crispant with R848 S64 L005 R1 001.fastq.gz   read2PairFiles=Rag1 crispant with R848 S64 L005 R2 001.fastq.gz   read3PairFiles=Rag1 crispant with R848 S64 L005 I1 001.fastq.gz   read4PairFiles=Rag1 crispant with R848 S64 L005 I2 001.fastq.gz,Rag1_crispant_with_R848_S64_L005_I1_001.fastq.gz Rag1_crispant_with_R848_S64_L005_I2_001.fastq.gz Rag1_crispant_with_R848_S64_L005_R1_001.fastq.gz Rag1_crispant_with_R848_S64_L005_R2_001.fastq.gz,fastq fastq fastq fastq,51690121264.0,371871376.0,GSM8864273 r1,0:28 1:91 2:10 3:10,A:9268291738;C:7690563124;G:8398909329;T:8480309041;N:2221984,28,91,10,10,9268291738,7690563124,8398909329,8480309041,2221984,SRX28117245,SRS24473023,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35486,SRR32834032,SRX28117244,SRS24473025,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  slc24a5 crispant  R848 treated,GSM8864272,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|genotype:slc24a5 mosaic mutant|treatment:Resiquimod R848 treated|geo loc name:missing|collection date:missing,mCherry cells  slc24a5 crispant  R848 treated,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells|genotype:slc24a5 mosaic mutant|treatment:Resiquimod R848 treated,GSM8864272,GSM8864272: mCherry cells  slc24a5 crispant  R848 treated; Danio rerio; RNA Seq,GSM8864272 r1,GSM8864272,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=slc24a5 crispant with R848 S62 L005 R1 001.fastq.gz   read2PairFiles=slc24a5 crispant with R848 S62 L005 R2 001.fastq.gz   read3PairFiles=slc24a5 crispant with R848 S62 L005 I1 001.fastq.gz   read4PairFiles=slc24a5 crispant with R848 S62 L005 I2 001.fastq.gz,slc24a5_crispant_with_R848_S62_L005_I1_001.fastq.gz slc24a5_crispant_with_R848_S62_L005_I2_001.fastq.gz slc24a5_crispant_with_R848_S62_L005_R1_001.fastq.gz slc24a5_crispant_with_R848_S62_L005_R2_001.fastq.gz,fastq fastq fastq fastq,67359016638.0,484597242.0,GSM8864272 r1,0:28 1:91 2:10 3:10,A:12101967291;C:10017190111;G:10977547337;T:10998758556;N:2885727,28,91,10,10,12101967291,10017190111,10977547337,10998758556,2885727,SRX28117244,SRS24473025,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35487,SRR32834033,SRX28117243,SRS24473024,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  rag1 crispant,GSM8864271,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|genotype:rag1 mosaic mutant|geo loc name:missing|collection date:missing,mCherry cells  rag1 crispant,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells|genotype:rag1 mosaic mutant,GSM8864271,GSM8864271: mCherry cells  rag1 crispant; Danio rerio; RNA Seq,GSM8864271 r1,GSM8864271,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=Rag1 crispant S63 L005 R1 001.fastq.gz   read2PairFiles=Rag1 crispant S63 L005 R2 001.fastq.gz   read3PairFiles=Rag1 crispant S63 L005 I1 001.fastq.gz   read4PairFiles=Rag1 crispant S63 L005 I2 001.fastq.gz,Rag1_crispant_S63_L005_I1_001.fastq.gz Rag1_crispant_S63_L005_I2_001.fastq.gz Rag1_crispant_S63_L005_R1_001.fastq.gz Rag1_crispant_S63_L005_R2_001.fastq.gz,fastq fastq fastq fastq,40550115550.0,291727450.0,GSM8864271 r1,0:28 1:91 2:10 3:10,A:7262987235;C:6078752458;G:6639990009;T:6563701562;N:1766686,28,91,10,10,7262987235,6078752458,6639990009,6563701562,1766686,SRX28117243,SRS24473024,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35488,SRR32834034,SRX28117242,SRS24473022,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  slc24a5 crispant,GSM8864270,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|genotype:slc24a5 mosaic mutant|geo loc name:missing|collection date:missing,mCherry cells  slc24a5 crispant,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells|genotype:slc24a5 mosaic mutant,GSM8864270,GSM8864270: mCherry cells  slc24a5 crispant; Danio rerio; RNA Seq,GSM8864270 r1,GSM8864270,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=slc24a5 crispant S61 L005 R1 001.fastq.gz   read2PairFiles=slc24a5 crispant S61 L005 R2 001.fastq.gz   read3PairFiles=slc24a5 crispant S61 L005 I1 001.fastq.gz   read4PairFiles=slc24a5 crispant S61 L005 I2 001.fastq.gz,slc24a5_crispant_S61_L005_I1_001.fastq.gz slc24a5_crispant_S61_L005_I2_001.fastq.gz slc24a5_crispant_S61_L005_R1_001.fastq.gz slc24a5_crispant_S61_L005_R2_001.fastq.gz,fastq fastq fastq fastq,53500554564.0,384896076.0,GSM8864270 r1,0:28 1:91 2:10 3:10,A:9607899809;C:8061049626;G:8772491787;T:8581787300;N:2314394,28,91,10,10,9607899809,8061049626,8772491787,8581787300,2314394,SRX28117242,SRS24473022,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35489,SRR32834035,SRX28117241,SRS24473017,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  runx1 homozygous mutants,GSM8864269,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|genotype:runx1 homozygous|geo loc name:missing|collection date:missing,mCherry cells  runx1 homozygous mutants,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells|genotype:runx1 homozygous,GSM8864269,GSM8864269: mCherry cells  runx1 homozygous mutants; Danio rerio; RNA Seq,GSM8864269 r1,GSM8864269,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=Runx1 Homz Mutants earlyHSPC trace 6 dpf S2 L002 R1 001.fastq.gz   read2PairFiles=Runx1 Homz Mutants earlyHSPC trace 6 dpf S2 L002 R2 001.fastq.gz   read3PairFiles=Runx1 Homz Mutants earlyHSPC trace 6 dpf S2 L002 I1 001.fastq.gz   read4PairFiles=Runx1 Homz Mutants earlyHSPC trace 6 dpf S2 L002 I2 001.fastq.gz,Runx1_Homz_Mutants_earlyHSPC_trace_6_dpf_S2_L002_I1_001.fastq.gz Runx1_Homz_Mutants_earlyHSPC_trace_6_dpf_S2_L002_I2_001.fastq.gz Runx1_Homz_Mutants_earlyHSPC_trace_6_dpf_S2_L002_R1_001.fastq.gz Runx1_Homz_Mutants_earlyHSPC_trace_6_dpf_S2_L002_R2_001.fastq.gz,fastq fastq fastq fastq,27845512960.0,87017228.0,GSM8864269 r1,0:150 1:150 2:10 3:10,A:4012440512;C:2615250336;G:3042659166;T:3381797139;N:437047,150,150,10,10,4012440512,2615250336,3042659166,3381797139,437047,SRX28117241,SRS24473017,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35490,SRR32834036,SRX28117240,SRS24473018,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  sibling controls,GSM8864268,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|genotype:wild type or runx1 heterozygous|geo loc name:missing|collection date:missing,mCherry cells  sibling controls,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells|genotype:wild type or runx1 heterozygous,GSM8864268,GSM8864268: mCherry cells  sibling controls; Danio rerio; RNA Seq,GSM8864268 r1,GSM8864268,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=Sibling Control earlyHSPC trace 6 dpf S1 L002 R1 001.fastq.gz   read2PairFiles=Sibling Control earlyHSPC trace 6 dpf S1 L002 R2 001.fastq.gz   read3PairFiles=Sibling Control earlyHSPC trace 6 dpf S1 L002 I1 001.fastq.gz   read4PairFiles=Sibling Control earlyHSPC trace 6 dpf S1 L002 I2 001.fastq.gz,Sibling_Control_earlyHSPC_trace_6_dpf_S1_L002_I1_001.fastq.gz Sibling_Control_earlyHSPC_trace_6_dpf_S1_L002_I2_001.fastq.gz Sibling_Control_earlyHSPC_trace_6_dpf_S1_L002_R1_001.fastq.gz Sibling_Control_earlyHSPC_trace_6_dpf_S1_L002_R2_001.fastq.gz,fastq fastq fastq fastq,24953253760.0,77978918.0,GSM8864268 r1,0:150 1:150 2:10 3:10,A:3390875336;C:2571521800;G:2871954356;T:2862416982;N:69226,150,150,10,10,3390875336,2571521800,2871954356,2862416982,69226,SRX28117240,SRS24473018,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35491,SRR32834037,SRX28117239,SRS24473015,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  late HSPCs 10 dpf,GSM8864267,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells  late HSPCs 10 dpf,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells,GSM8864267,GSM8864267: mCherry cells  late HSPCs 10 dpf; Danio rerio; RNA Seq,GSM8864267 r1,GSM8864267,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=lateHSPC trace at 10dpf S1 L003 R1 001.fastq.gz   read2PairFiles=lateHSPC trace at 10dpf S1 L003 R2 001.fastq.gz   read3PairFiles=lateHSPC trace at 10dpf S1 L003 I1 001.fastq.gz   read4PairFiles=lateHSPC trace at 10dpf S1 L003 I2 001.fastq.gz,lateHSPC_trace_at_10dpf_S1_L003_I1_001.fastq.gz lateHSPC_trace_at_10dpf_S1_L003_I2_001.fastq.gz lateHSPC_trace_at_10dpf_S1_L003_R1_001.fastq.gz lateHSPC_trace_at_10dpf_S1_L003_R2_001.fastq.gz,fastq fastq fastq fastq,49750537600.0,155470430.0,GSM8864267 r1,0:150 1:150 2:10 3:10,A:6695708919;C:5110107098;G:5648204020;T:5864962224;N:1582239,150,150,10,10,6695708919,5110107098,5648204020,5864962224,1582239,SRX28117239,SRS24473015,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35492,SRR32834038,SRX28117239,SRS24473015,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  late HSPCs 10 dpf,GSM8864267,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells  late HSPCs 10 dpf,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells,GSM8864267,GSM8864267: mCherry cells  late HSPCs 10 dpf; Danio rerio; RNA Seq,GSM8864267 r1,GSM8864267,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=lateHSPC trace at 10dpf S18 L002 R1 001.fastq.gz   read2PairFiles=lateHSPC trace at 10dpf S18 L002 R2 001.fastq.gz   read3PairFiles=lateHSPC trace at 10dpf S18 L002 I1 001.fastq.gz   read4PairFiles=lateHSPC trace at 10dpf S18 L002 I2 001.fastq.gz,lateHSPC_trace_at_10dpf_S18_L002_I1_001.fastq.gz lateHSPC_trace_at_10dpf_S18_L002_I2_001.fastq.gz lateHSPC_trace_at_10dpf_S18_L002_R1_001.fastq.gz lateHSPC_trace_at_10dpf_S18_L002_R2_001.fastq.gz,fastq fastq fastq fastq,3818546250.0,27670625.0,GSM8864267 r2,0:28 1:90 2:10 3:10,A:716133237;C:554493684;G:608989896;T:610460128;N:279305,28,90,10,10,716133237,554493684,608989896,610460128,279305,SRX28117239,SRS24473015,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35493,SRR32834039,SRX28117238,SRS24473019,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  late HSPCs 6 dpf,GSM8864266,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells  late HSPCs 6 dpf,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells,GSM8864266,GSM8864266: mCherry cells  late HSPCs 6 dpf; Danio rerio; RNA Seq,GSM8864266 r1,GSM8864266,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=lateHSPC trace at 6dpf S17 L002 R1 001.fastq.gz   read2PairFiles=lateHSPC trace at 6dpf S17 L002 R2 001.fastq.gz   read3PairFiles=lateHSPC trace at 6dpf S17 L002 I1 001.fastq.gz   read4PairFiles=lateHSPC trace at 6dpf S17 L002 I2 001.fastq.gz,lateHSPC_trace_at_6dpf_S17_L002_I1_001.fastq.gz lateHSPC_trace_at_6dpf_S17_L002_I2_001.fastq.gz lateHSPC_trace_at_6dpf_S17_L002_R1_001.fastq.gz lateHSPC_trace_at_6dpf_S17_L002_R2_001.fastq.gz,fastq fastq fastq fastq,12871712088.0,93273276.0,GSM8864266 r1,0:28 1:90 2:10 3:10,A:2421583617;C:1888963122;G:2078815965;T:2004213972;N:1018164,28,90,10,10,2421583617,1888963122,2078815965,2004213972,1018164,SRX28117238,SRS24473019,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35494,SRR32834040,SRX28117237,SRS24473014,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  late HSPCs 4 dpf,GSM8864265,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells  late HSPCs 4 dpf,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells,GSM8864265,GSM8864265: mCherry cells  late HSPCs 4 dpf; Danio rerio; RNA Seq,GSM8864265 r1,GSM8864265,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=lateHSPC trace at 4dpf S16 L002 R1 001.fastq.gz   read2PairFiles=lateHSPC trace at 4dpf S16 L002 R2 001.fastq.gz   read3PairFiles=lateHSPC trace at 4dpf S16 L002 I1 001.fastq.gz   read4PairFiles=lateHSPC trace at 4dpf S16 L002 I2 001.fastq.gz,lateHSPC_trace_at_4dpf_S16_L002_I1_001.fastq.gz lateHSPC_trace_at_4dpf_S16_L002_I2_001.fastq.gz lateHSPC_trace_at_4dpf_S16_L002_R1_001.fastq.gz lateHSPC_trace_at_4dpf_S16_L002_R2_001.fastq.gz,fastq fastq fastq fastq,11138275734.0,80712143.0,GSM8864265 r1,0:28 1:90 2:10 3:10,A:2022661838;C:1679042427;G:1720706851;T:1840857883;N:823871,28,90,10,10,2022661838,1679042427,1720706851,1840857883,823871,SRX28117237,SRS24473014,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35495,SRR32834041,SRX28117236,SRS24473016,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  mid HSPCs 10 dpf,GSM8864264,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells  mid HSPCs 10 dpf,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells,GSM8864264,GSM8864264: mCherry cells  mid HSPCs 10 dpf; Danio rerio; RNA Seq,GSM8864264 r1,GSM8864264,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=midHSPC 10dpf S1 L001 R1 001.fastq.gz   read2PairFiles=midHSPC 10dpf S1 L001 R2 001.fastq.gz   read3PairFiles=midHSPC 10dpf S1 L001 I1 001.fastq.gz   read4PairFiles=midHSPC 10dpf S1 L001 I2 001.fastq.gz,midHSPC_10dpf_S1_L001_I1_001.fastq.gz midHSPC_10dpf_S1_L001_I2_001.fastq.gz midHSPC_10dpf_S1_L001_R1_001.fastq.gz midHSPC_10dpf_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,211217834240.0,660055732.0,GSM8864264 r1,0:150 1:150 2:10 3:10,A:28426769480;C:22300370613;G:24520861829;T:23758933345;N:1424533,150,150,10,10,28426769480,22300370613,24520861829,23758933345,1424533,SRX28117236,SRS24473016,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35496,SRR32834042,SRX28117235,SRS24473020,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  mid HSPCs 6 dpf,GSM8864263,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells  mid HSPCs 6 dpf,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells,GSM8864263,GSM8864263: mCherry cells  mid HSPCs 6 dpf; Danio rerio; RNA Seq,GSM8864263 r1,GSM8864263,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=midHSPC 6dpf S1 L001 R1 001.fastq.gz   read2PairFiles=midHSPC 6dpf S1 L001 R2 001.fastq.gz   read3PairFiles=midHSPC 6dpf S1 L001 I1 001.fastq.gz   read4PairFiles=midHSPC 6dpf S1 L001 I2 001.fastq.gz,midHSPC_6dpf_S1_L001_I1_001.fastq.gz midHSPC_6dpf_S1_L001_I2_001.fastq.gz midHSPC_6dpf_S1_L001_R1_001.fastq.gz midHSPC_6dpf_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,241173414720.0,753666921.0,GSM8864263 r1,,,,,,,,,,,,SRX28117235,SRS24473020,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,1,0.94667,,0.08748,,0.83881,,0.5015,,150,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35497,SRR32834043,SRX28117234,SRS24473021,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  mid HSPCs 3 dpf,GSM8864262,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells  mid HSPCs 3 dpf,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells,GSM8864262,GSM8864262: mCherry cells  mid HSPCs 3 dpf; Danio rerio; RNA Seq,GSM8864262 r1,GSM8864262,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=midHSPC 3dpf S6 L003 R1 001.fastq.gz   read2PairFiles=midHSPC 3dpf S6 L003 R2 001.fastq.gz   read3PairFiles=midHSPC 3dpf S6 L003 I1 001.fastq.gz   read4PairFiles=midHSPC 3dpf S6 L003 I2 001.fastq.gz,midHSPC_3dpf_S6_L003_I1_001.fastq.gz midHSPC_3dpf_S6_L003_I2_001.fastq.gz midHSPC_3dpf_S6_L003_R1_001.fastq.gz midHSPC_3dpf_S6_L003_R2_001.fastq.gz,fastq fastq fastq fastq,71933359680.0,224791749.0,GSM8864262 r1,0:150 1:150 2:10 3:10,A:9519625855;C:6982221178;G:8366028895;T:7767873072;N:1083013350,150,150,10,10,9519625855,6982221178,8366028895,7767873072,1083013350,SRX28117234,SRS24473021,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,1,0.78368,,0.08584,,0.82144,,0.50936,,150,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35498,SRR32834044,SRX28117233,SRS24473012,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  early HSPCs 10 dpf,GSM8864261,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells  early HSPCs 10 dpf,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells,GSM8864261,GSM8864261: mCherry cells  early HSPCs 10 dpf; Danio rerio; RNA Seq,GSM8864261 r1,GSM8864261,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=earlyHSPC 10dpf S1 L001 R1 001.fastq.gz   read2PairFiles=earlyHSPC 10dpf S1 L001 R2 001.fastq.gz   read3PairFiles=earlyHSPC 10dpf S1 L001 I1 001.fastq.gz   read4PairFiles=earlyHSPC 10dpf S1 L001 I2 001.fastq.gz,earlyHSPC_10dpf_S1_L001_I1_001.fastq.gz earlyHSPC_10dpf_S1_L001_I2_001.fastq.gz earlyHSPC_10dpf_S1_L001_R1_001.fastq.gz earlyHSPC_10dpf_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,267665197120.0,836453741.0,GSM8864261 r1,,,,,,,,,,,,SRX28117233,SRS24473012,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35499,SRR32834045,SRX28117232,SRS24473013,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  early HSPCs 6 dpf,GSM8864260,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells  early HSPCs 6 dpf,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells,GSM8864260,GSM8864260: mCherry cells  early HSPCs 6 dpf; Danio rerio; RNA Seq,GSM8864260 r1,GSM8864260,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=earlyHSPC 6dpf S1 L001 R1 001.fastq.gz   read2PairFiles=earlyHSPC 6dpf S1 L001 R2 001.fastq.gz   read3PairFiles=earlyHSPC 6dpf S1 L001 I1 001.fastq.gz   read4PairFiles=earlyHSPC 6dpf S1 L001 I2 001.fastq.gz,earlyHSPC_6dpf_S1_L001_I1_001.fastq.gz earlyHSPC_6dpf_S1_L001_I2_001.fastq.gz earlyHSPC_6dpf_S1_L001_R1_001.fastq.gz earlyHSPC_6dpf_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,234759123200.0,733622260.0,GSM8864260 r1,,,,,,,,,,,,SRX28117232,SRS24473013,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35500,SRR32834046,SRX28117231,SRS24473011,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  early HSPCs 2 dpf,GSM8864259,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells  early HSPCs 2 dpf,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells,GSM8864259,GSM8864259: mCherry cells  early HSPCs 2 dpf; Danio rerio; RNA Seq,GSM8864259 r1,GSM8864259,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=earlyHSPC 2dpf S5 L003 R1 001.fastq.gz   read2PairFiles=earlyHSPC 2dpf S5 L003 R2 001.fastq.gz   read3PairFiles=earlyHSPC 2dpf S5 L003 I1 001.fastq.gz   read4PairFiles=earlyHSPC 2dpf S5 L003 I2 001.fastq.gz,earlyHSPC_2dpf_S5_L003_I1_001.fastq.gz earlyHSPC_2dpf_S5_L003_I2_001.fastq.gz earlyHSPC_2dpf_S5_L003_R1_001.fastq.gz earlyHSPC_2dpf_S5_L003_R2_001.fastq.gz,fastq fastq fastq fastq,80730897280.0,252284054.0,GSM8864259 r1,0:150 1:150 2:10 3:10,A:10564796609;C:7860706889;G:9394625294;T:8808848403;N:1213630905,150,150,10,10,10564796609,7860706889,9394625294,8808848403,1213630905,SRX28117231,SRS24473011,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Multi-stage,Multi-stage,Blood,Hematopoietic System
53001,SRR12173589,SRX8688333,SRS6966994,SRP213938,PRJNA553572,A map of cis regulatory elements and 3D genome structures in zebrafish,GSE134055,Other,The zebrafish has been widely used for the study of human disease and development  as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome  however  has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects  we performed RNA seq  ATAC seq  ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall  we have identified 235 596 cis regulatory elements  which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish  human  and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore  through the analysis of Hi C data in zebrafish brain and muscle  we observed different levels of 3D genome organization  including compartment  topological associating domains TADs  and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and  embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3  RNA Seq  11 of them were examined using ATAC seq  WGBS and ChIP seq H3K9me3 and H3K9me2  and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that  for the samples GSM4661977 GSM4662088  [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.,,pubmed:33239788;pubmed:35649578,,YueLab RNA seq Blood rep2,GSM4662086,,source name:YueLab RNA seq Blood|strain:Tuebingen|tissue:Blood,YueLab RNA seq Blood rep2,RNA seq reads were aligned to zv10 genome assembly using STAR; The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using Bowtie2;H3K27ac  H3K4me3 ChIP seq were called using MACS2 with the following  setting: ChIP seq q value <10e 2  p value<10e 5  Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5.For the ATAC seq  the peak length were fixed to 500 bp. We only selected the peak with the most significant signal if several peaks overlap with each other in each tissue.Since the H3K9me3 and H3K9me2 makers are broad domain  we called the peak using Homer with the parameter “ region  size 1000”  and peaks within 5 kb were merged together. HiC matrix was generated using HiC Pro WGBS data were mapped to in silico bisulfite converted zebrafish genome reference by using Bismark For the scATAC seq  the BCL files generated from sequencing were used as inputs to the 10X Genomics Cell Ranger ATAC seq pipeline; then the FASTQ files were aligned to the GRCz10 genome using BWA and the fragments with MAPQ>30 were kept for further analysis and each fragment is associated with a single cell barcode. Genome build: zv10GRCz10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged,YueLab RNA seq Blood,,RNA seq: For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. RNA seq: The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly  polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. ChIP seq: All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 µL of ChIP seq lysis buffer 20 mM Tris HCl  pH 8.0  1% SDS  50 mM EDTA  1X proteinase inhibitor cocktail. Next  900 µL cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W  duty factor 5  200 per burst. Sonication time is variable  depending on tissue types. To check the chromatin fragmentation size  20 µL of input chromatin was reverse crosslinked in elution buffer 20 mM Tris HCl  pH 8.0  1% SDS  1 mM EDTA at 65 °C overnight  treated with Rnase A and proteinase K and purified by phenol chloroform extraction. Input DNA was then loaded on a Lonza flash gel to make sure that the majority of DNA size distributes between 100 300 bp. To prepare antibody beads complex  3 µg of histone H3K27ac antibody Active Motif  39133 or H3K4me3 antibody EMD Millipore  07 473 was mix with 12 µL M 280 sheep anti rabbit IgG Dynabeads ThermoFisher  11203D in 150 µL of 5 mg/mL BSA/1X PBS buffer  with rotation at 4 °C for 3 h. post incubation  antibody beads complex was washed once with BSA/1X PBS buffer. About 200 µg chromatin was used per IP. Equal volume of master mix 1X TE  2% Triton X 100  0.2% sodium deoxycholate  2X proteinase inhibitor cocktail was mixed with 200 µg chromatin and then incubated with antibody beads complex overnight with rotation. The next morning  the beads were washed 5 times with cold RIPA wash buffer 20 mM Tris HCl  pH 8.0  1% NP 40  0.7% sodium deoxycholate  500 mM LiCl  1 mM EDTA  1X proteinase inhibitor cocktail. Then the chromatin bound on the beads was eluted by 150 µL of elution buffer at 65 °C for 30 min. ChIP seq: To prepare the library  eluted chromatin was reverse crosslinked and purified by phenol chloroform extraction. Then DNA was end repaired by END IT DNA end repair kit Epicentre  ER81050 according to kit’s protocol  added A using Klenow  fragment 3’ >5’ exo  NEB  M0212S  ligated with Illumina TruSeq adaptor Illumina  FC 121 3001 and subsequently amplified by PCR Roche  kk2601. The quality and quantity of all the libraries were checked using BioAnalyzer High Sensitivity DNA Kit Agilent. The libraries were sequenced on Illumina HiSeq 2500 with reads length of 2X 50 bp or 2X 100 bp. ATAC seq: Tuebingen adult tissues were ground in liquid nitrogen resuspended in 1 mL of lysis buffer 1X PBS  0.2% NP 40  5% BSA  1 mM DTT  protease inhibitors  followed by incubation at  4 °C for 10 min on an overhead shaker. post that  lysate was filtered through 40 m cell strainer and nuclei were collected at 1000X g for 5 min. ATAC seq: Tagmentation was performed immediately according to ATAC seq protocol reported previouslyBuenrostro et al.  2013 Hi C: For brain tissue  two adult Tuebingen brains were slightly ground into small granules in liquid nitrogen and resuspended in 1 mL of cold hypotonic buffer 20 mM Tris HCl  pH 8.0  10 mM NaCl  20 mM EDTA. Granular brains were then dounce homogenized with loose pestle for 20 times. The top of the homogenate was carefully transferred into a new tube and fixed with 2% formaldehyde at room temperature for 10 min. 0.2 M of glycine was added to stop fixation. For muscle tissue  60 mg of Tuebingen muscle was first chopped into small pieces and digested by 0.25% trypsin at room temperature for 30 min. post neutralization with FBS  muscle cells were resuspended in cold 1X PBS and fixed with 2% of formaldehyde at room temperature for 10 min. 0.2 M glycine was then added to stop fixation. Hi C: Hi C experiments on adult zebrafish brain and muscle tissues were performed according to previously published protocolRao et al.  2014. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 100 bp high throughput sequencing using HiSeq 2500  or HiSeq 4000Illumina. WGBS: Tübingen adult tissues were dissected  and the genomic DNA was extracted using DNeasy Blood & Tissue Kit Qiagen  69504. Then 1 µg of genomic DNA of each adult tissue was subjected to bisulfite conversion using EZ DNA Methylation Gold Kits WGBS: The final libraries were prepared using the Accel NGS® Methyl Seq DNA Library Kit. scATAC seq: Single cell ATAC seq scATAC seq was performed in one female brain and one male brain  respectively  on the 10X Genomics platform. To isolate nuclei  freshly dissected single brain was transferred to 1 mL NbActiv1 medium BrainBits  NbActiv1 500 with a wide bore pipette tip to break the tissue into small pieces. Then the tissue was broken up completely using regular bore pipette tips followed by filtering through a 30 µm cell strainer. The isolated cells were spun down at 500 g for 5 min at 4 °C and then lysed in 100 µL chilled 0.1X Lysis Buffer 10 mM Tris HCl  pH 7.5  10 mM NaCl  3 mM MgCl2  1% BSA 0.01% Tween 20  0.01% NP40 and 0.001% digitonin on ice for 5 min. Then 1 mL chilled Wash Buffer 10 mM Tris HCl  pH 7.5  10 mM NaCl  3 mM MgCl2  1% BSA  0.1% Tween 20 was added to the lysed cells and cells were spun down at 500 g for 5 min at 4 °C. At last  300 µL chilled Diluted Nuclei Buffer 10x Genomics  PN 2000153/2000207 was added to resuspend the nuclei. The nuclei were filtered again using a 30 µm cell strainer before cell counting scATAC seq: Around 12 000 nuclei were used for one Tn5 tagmentation reaction  and the scATAC seq library was prepared and sequenced exactly according to the company’s user guide.,RNA seq: Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions ChIP seq  ATAC seq  Hi C and WGBS: Ault Tuebingen zebrafish were raised under standard laboratory conditions,strain:Tuebingen|tissue:Blood,GSM4662086,GSM4662086: YueLab RNA seq Blood rep2; Danio rerio; RNA Seq,GSM4662086,,1,RNA seq: For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. RNA seq: The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly  polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. ChIP seq: All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 µL of ChIP seq lysis buffer 20 mM Tris HCl  pH 8.0  1% SDS  50 mM EDTA  1X proteinase inhibitor cocktail. Next  900 µL cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W  duty factor 5  200 per burst. Sonication time is variable  depending on tissue types. To check the chromatin fragmentation size  20 µL of input chromatin was reverse crosslinked in elution buffer 20 mM Tris HCl  pH 8.0  1% SDS  1 mM EDTA at 65 °C overnight  treated with Rnase A and proteinase K and purified by phenol chloroform extraction. Input DNA was then loaded on a Lonza flash gel to make sure that the majority of DNA size distributes between 100 300 bp. To prepare antibody beads complex  3 µg of histone H3K27ac antibody Active Motif  39133 or H3K4me3 antibody EMD Millipore  07 473 was mix with 12 µL M 280 sheep anti rabbit IgG Dynabeads ThermoFisher  11203D in 150 µL of 5 mg/mL BSA/1X PBS buffer  with rotation at 4 °C for 3 h. post incubation  antibody beads complex was washed once with BSA/1X PBS buffer. About 200 µg chromatin was used per IP. Equal volume of master mix 1X TE  2% Triton X 100  0.2% sodium deoxycholate  2X proteinase inhibitor cocktail was mixed with 200 µg chromatin and then incubated with antibody beads complex overnight with rotation. The next morning  the beads were washed 5 times with cold RIPA wash buffer 20 mM Tris HCl  pH 8.0  1% NP 40  0.7% sodium deoxycholate  500 mM LiCl  1 mM EDTA  1X proteinase inhibitor cocktail. Then the chromatin bound on the beads was eluted by 150 µL of elution buffer at 65 °C for 30 min. ChIP seq: To prepare the library  eluted chromatin was reverse crosslinked and purified by phenol chloroform extraction. Then DNA was end repaired by END IT DNA end repair kit Epicentre  ER81050 according to kit's protocol  added A using Klenow  fragment three prime >five prime exo  NEB  M0212S  ligated with Illumina TruSeq adaptor Illumina  FC 121 3001 and subsequently amplified by PCR Roche  kk2601. The quality and quantity of all the libraries were checked using BioAnalyzer High Sensitivity DNA Kit Agilent. The libraries were sequenced on Illumina HiSeq 2500 with reads length of 2X 50 bp or 2X 100 bp. ATAC seq: Tuebingen adult tissues were ground in liquid nitrogen resuspended in 1 mL of lysis buffer 1X PBS  0.2% NP 40  5% BSA  1 mM DTT  protease inhibitors  followed by incubation at  4 °C for 10 min on an overhead shaker. post that  lysate was filtered through 40 m cell strainer and nuclei were collected at 1000X g for 5 min. ATAC seq: Tagmentation was performed immediately according to ATAC seq protocol reported previouslyBuenrostro et al.  2013 Hi C: For brain tissue  two adult Tuebingen brains were slightly ground into small granules in liquid nitrogen and resuspended in 1 mL of cold hypotonic buffer 20 mM Tris HCl  pH 8.0  10 mM NaCl  20 mM EDTA. Granular brains were then dounce homogenized with loose pestle for 20 times. The top of the homogenate was carefully transferred into a new tube and fixed with 2% formaldehyde at room temperature for 10 min. 0.2 M of glycine was added to stop fixation. For muscle tissue  60 mg of Tuebingen muscle was first chopped into small pieces and digested by 0.25% trypsin at room temperature for 30 min. post neutralization with FBS  muscle cells were resuspended in cold 1X PBS and fixed with 2% of formaldehyde at room temperature for 10 min. 0.2 M glycine was then added to stop fixation. Hi C: Hi C experiments on adult zebrafish brain and muscle tissues were performed according to previously published protocolRao et al.  2014. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 100 bp high throughput sequencing using HiSeq 2500  or HiSeq 4000Illumina. WGBS: Tübingen adult tissues were dissected  and the genomic DNA was extracted using DNeasy Blood & Tissue Kit Qiagen  69504. Then 1 µg of genomic DNA of each adult tissue was subjected to bisulfite conversion using EZ DNA Methylation Gold Kits WGBS: The final libraries were prepared using the Accel NGS® Methyl Seq DNA Library Kit. scATAC seq: Single cell ATAC seq scATAC seq was performed in one female brain and one male brain  respectively  on the 10X Genomics platform. To isolate nuclei  freshly dissected single brain was transferred to 1 mL NbActiv1 medium BrainBits  NbActiv1 500 with a wide bore pipette tip to break the tissue into small pieces. Then the tissue was broken up completely using regular bore pipette tips followed by filtering through a 30 µm cell strainer. The isolated cells were spun down at 500 g for 5 min at 4 °C and then lysed in 100 µL chilled 0.1X Lysis Buffer 10 mM Tris HCl  pH 7.5  10 mM NaCl  3 mM MgCl2  1% BSA 0.01% Tween 20  0.01% NP40 and 0.001% digitonin on ice for 5 min. Then 1 mL chilled Wash Buffer 10 mM Tris HCl  pH 7.5  10 mM NaCl  3 mM MgCl2  1% BSA  0.1% Tween 20 was added to the lysed cells and cells were spun down at 500 g for 5 min at 4 °C. At last  300 µL chilled Diluted Nuclei Buffer 10x Genomics  PN 2000153/2000207 was added to resuspend the nuclei. The nuclei were filtered again using a 30 µm cell strainer before cell counting scATAC seq: Around 12 000 nuclei were used for one Tn5 tagmentation reaction  and the scATAC seq library was prepared and sequenced exactly according to the company's user guide.,GEO Accession:GSM4662086,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP213938,,,YueLab-RNA-seq-Blood-rep2_2.fastq.gz YueLab-RNA-seq-Blood-rep2_1.fastq.gz,fastq fastq,9750305560.0,32285780.0,GSM4662086 r1,0:151 1:151,A:2564237490;C:2313022617;G:2328740350;T:2544206938;N:98165,151,151,,,2564237490,2313022617,2328740350,2544206938,98165,SRX8688333,SRS6966994,SRA919194,GEO,"Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine",2,0.90976,0.90587,0.07014,0.06953,0.85415,0.85624,0.51898,0.51696,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,sc,single_cell_droplet,10x,,United States,2020-07-08,Pharyngula,Embryo,Blood,Hematopoietic System
53002,SRR12173588,SRX8688332,SRS6966993,SRP213938,PRJNA553572,A map of cis regulatory elements and 3D genome structures in zebrafish,GSE134055,Other,The zebrafish has been widely used for the study of human disease and development  as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome  however  has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects  we performed RNA seq  ATAC seq  ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall  we have identified 235 596 cis regulatory elements  which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish  human  and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore  through the analysis of Hi C data in zebrafish brain and muscle  we observed different levels of 3D genome organization  including compartment  topological associating domains TADs  and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and  embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3  RNA Seq  11 of them were examined using ATAC seq  WGBS and ChIP seq H3K9me3 and H3K9me2  and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that  for the samples GSM4661977 GSM4662088  [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.,,pubmed:33239788;pubmed:35649578,,YueLab RNA seq Blood rep1,GSM4662085,,source name:YueLab RNA seq Blood|strain:Tuebingen|tissue:Blood,YueLab RNA seq Blood rep1,RNA seq reads were aligned to zv10 genome assembly using STAR; The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using Bowtie2;H3K27ac  H3K4me3 ChIP seq were called using MACS2 with the following  setting: ChIP seq q value <10e 2  p value<10e 5  Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5.For the ATAC seq  the peak length were fixed to 500 bp. We only selected the peak with the most significant signal if several peaks overlap with each other in each tissue.Since the H3K9me3 and H3K9me2 makers are broad domain  we called the peak using Homer with the parameter “ region  size 1000”  and peaks within 5 kb were merged together. HiC matrix was generated using HiC Pro WGBS data were mapped to in silico bisulfite converted zebrafish genome reference by using Bismark For the scATAC seq  the BCL files generated from sequencing were used as inputs to the 10X Genomics Cell Ranger ATAC seq pipeline; then the FASTQ files were aligned to the GRCz10 genome using BWA and the fragments with MAPQ>30 were kept for further analysis and each fragment is associated with a single cell barcode. Genome build: zv10GRCz10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged,YueLab RNA seq Blood,,RNA seq: For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. RNA seq: The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly  polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. ChIP seq: All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 µL of ChIP seq lysis buffer 20 mM Tris HCl  pH 8.0  1% SDS  50 mM EDTA  1X proteinase inhibitor cocktail. Next  900 µL cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W  duty factor 5  200 per burst. Sonication time is variable  depending on tissue types. To check the chromatin fragmentation size  20 µL of input chromatin was reverse crosslinked in elution buffer 20 mM Tris HCl  pH 8.0  1% SDS  1 mM EDTA at 65 °C overnight  treated with Rnase A and proteinase K and purified by phenol chloroform extraction. Input DNA was then loaded on a Lonza flash gel to make sure that the majority of DNA size distributes between 100 300 bp. To prepare antibody beads complex  3 µg of histone H3K27ac antibody Active Motif  39133 or H3K4me3 antibody EMD Millipore  07 473 was mix with 12 µL M 280 sheep anti rabbit IgG Dynabeads ThermoFisher  11203D in 150 µL of 5 mg/mL BSA/1X PBS buffer  with rotation at 4 °C for 3 h. post incubation  antibody beads complex was washed once with BSA/1X PBS buffer. About 200 µg chromatin was used per IP. Equal volume of master mix 1X TE  2% Triton X 100  0.2% sodium deoxycholate  2X proteinase inhibitor cocktail was mixed with 200 µg chromatin and then incubated with antibody beads complex overnight with rotation. The next morning  the beads were washed 5 times with cold RIPA wash buffer 20 mM Tris HCl  pH 8.0  1% NP 40  0.7% sodium deoxycholate  500 mM LiCl  1 mM EDTA  1X proteinase inhibitor cocktail. Then the chromatin bound on the beads was eluted by 150 µL of elution buffer at 65 °C for 30 min. ChIP seq: To prepare the library  eluted chromatin was reverse crosslinked and purified by phenol chloroform extraction. Then DNA was end repaired by END IT DNA end repair kit Epicentre  ER81050 according to kit’s protocol  added A using Klenow  fragment 3’ >5’ exo  NEB  M0212S  ligated with Illumina TruSeq adaptor Illumina  FC 121 3001 and subsequently amplified by PCR Roche  kk2601. The quality and quantity of all the libraries were checked using BioAnalyzer High Sensitivity DNA Kit Agilent. The libraries were sequenced on Illumina HiSeq 2500 with reads length of 2X 50 bp or 2X 100 bp. ATAC seq: Tuebingen adult tissues were ground in liquid nitrogen resuspended in 1 mL of lysis buffer 1X PBS  0.2% NP 40  5% BSA  1 mM DTT  protease inhibitors  followed by incubation at  4 °C for 10 min on an overhead shaker. post that  lysate was filtered through 40 m cell strainer and nuclei were collected at 1000X g for 5 min. ATAC seq: Tagmentation was performed immediately according to ATAC seq protocol reported previouslyBuenrostro et al.  2013 Hi C: For brain tissue  two adult Tuebingen brains were slightly ground into small granules in liquid nitrogen and resuspended in 1 mL of cold hypotonic buffer 20 mM Tris HCl  pH 8.0  10 mM NaCl  20 mM EDTA. Granular brains were then dounce homogenized with loose pestle for 20 times. The top of the homogenate was carefully transferred into a new tube and fixed with 2% formaldehyde at room temperature for 10 min. 0.2 M of glycine was added to stop fixation. For muscle tissue  60 mg of Tuebingen muscle was first chopped into small pieces and digested by 0.25% trypsin at room temperature for 30 min. post neutralization with FBS  muscle cells were resuspended in cold 1X PBS and fixed with 2% of formaldehyde at room temperature for 10 min. 0.2 M glycine was then added to stop fixation. Hi C: Hi C experiments on adult zebrafish brain and muscle tissues were performed according to previously published protocolRao et al.  2014. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 100 bp high throughput sequencing using HiSeq 2500  or HiSeq 4000Illumina. WGBS: Tübingen adult tissues were dissected  and the genomic DNA was extracted using DNeasy Blood & Tissue Kit Qiagen  69504. Then 1 µg of genomic DNA of each adult tissue was subjected to bisulfite conversion using EZ DNA Methylation Gold Kits WGBS: The final libraries were prepared using the Accel NGS® Methyl Seq DNA Library Kit. scATAC seq: Single cell ATAC seq scATAC seq was performed in one female brain and one male brain  respectively  on the 10X Genomics platform. To isolate nuclei  freshly dissected single brain was transferred to 1 mL NbActiv1 medium BrainBits  NbActiv1 500 with a wide bore pipette tip to break the tissue into small pieces. Then the tissue was broken up completely using regular bore pipette tips followed by filtering through a 30 µm cell strainer. The isolated cells were spun down at 500 g for 5 min at 4 °C and then lysed in 100 µL chilled 0.1X Lysis Buffer 10 mM Tris HCl  pH 7.5  10 mM NaCl  3 mM MgCl2  1% BSA 0.01% Tween 20  0.01% NP40 and 0.001% digitonin on ice for 5 min. Then 1 mL chilled Wash Buffer 10 mM Tris HCl  pH 7.5  10 mM NaCl  3 mM MgCl2  1% BSA  0.1% Tween 20 was added to the lysed cells and cells were spun down at 500 g for 5 min at 4 °C. At last  300 µL chilled Diluted Nuclei Buffer 10x Genomics  PN 2000153/2000207 was added to resuspend the nuclei. The nuclei were filtered again using a 30 µm cell strainer before cell counting scATAC seq: Around 12 000 nuclei were used for one Tn5 tagmentation reaction  and the scATAC seq library was prepared and sequenced exactly according to the company’s user guide.,RNA seq: Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions ChIP seq  ATAC seq  Hi C and WGBS: Ault Tuebingen zebrafish were raised under standard laboratory conditions,strain:Tuebingen|tissue:Blood,GSM4662085,GSM4662085: YueLab RNA seq Blood rep1; Danio rerio; RNA Seq,GSM4662085,,1,RNA seq: For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. RNA seq: The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly  polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. ChIP seq: All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 µL of ChIP seq lysis buffer 20 mM Tris HCl  pH 8.0  1% SDS  50 mM EDTA  1X proteinase inhibitor cocktail. Next  900 µL cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W  duty factor 5  200 per burst. Sonication time is variable  depending on tissue types. To check the chromatin fragmentation size  20 µL of input chromatin was reverse crosslinked in elution buffer 20 mM Tris HCl  pH 8.0  1% SDS  1 mM EDTA at 65 °C overnight  treated with Rnase A and proteinase K and purified by phenol chloroform extraction. Input DNA was then loaded on a Lonza flash gel to make sure that the majority of DNA size distributes between 100 300 bp. To prepare antibody beads complex  3 µg of histone H3K27ac antibody Active Motif  39133 or H3K4me3 antibody EMD Millipore  07 473 was mix with 12 µL M 280 sheep anti rabbit IgG Dynabeads ThermoFisher  11203D in 150 µL of 5 mg/mL BSA/1X PBS buffer  with rotation at 4 °C for 3 h. post incubation  antibody beads complex was washed once with BSA/1X PBS buffer. About 200 µg chromatin was used per IP. Equal volume of master mix 1X TE  2% Triton X 100  0.2% sodium deoxycholate  2X proteinase inhibitor cocktail was mixed with 200 µg chromatin and then incubated with antibody beads complex overnight with rotation. The next morning  the beads were washed 5 times with cold RIPA wash buffer 20 mM Tris HCl  pH 8.0  1% NP 40  0.7% sodium deoxycholate  500 mM LiCl  1 mM EDTA  1X proteinase inhibitor cocktail. Then the chromatin bound on the beads was eluted by 150 µL of elution buffer at 65 °C for 30 min. ChIP seq: To prepare the library  eluted chromatin was reverse crosslinked and purified by phenol chloroform extraction. Then DNA was end repaired by END IT DNA end repair kit Epicentre  ER81050 according to kit's protocol  added A using Klenow  fragment three prime >five prime exo  NEB  M0212S  ligated with Illumina TruSeq adaptor Illumina  FC 121 3001 and subsequently amplified by PCR Roche  kk2601. The quality and quantity of all the libraries were checked using BioAnalyzer High Sensitivity DNA Kit Agilent. The libraries were sequenced on Illumina HiSeq 2500 with reads length of 2X 50 bp or 2X 100 bp. ATAC seq: Tuebingen adult tissues were ground in liquid nitrogen resuspended in 1 mL of lysis buffer 1X PBS  0.2% NP 40  5% BSA  1 mM DTT  protease inhibitors  followed by incubation at  4 °C for 10 min on an overhead shaker. post that  lysate was filtered through 40 m cell strainer and nuclei were collected at 1000X g for 5 min. ATAC seq: Tagmentation was performed immediately according to ATAC seq protocol reported previouslyBuenrostro et al.  2013 Hi C: For brain tissue  two adult Tuebingen brains were slightly ground into small granules in liquid nitrogen and resuspended in 1 mL of cold hypotonic buffer 20 mM Tris HCl  pH 8.0  10 mM NaCl  20 mM EDTA. Granular brains were then dounce homogenized with loose pestle for 20 times. The top of the homogenate was carefully transferred into a new tube and fixed with 2% formaldehyde at room temperature for 10 min. 0.2 M of glycine was added to stop fixation. For muscle tissue  60 mg of Tuebingen muscle was first chopped into small pieces and digested by 0.25% trypsin at room temperature for 30 min. post neutralization with FBS  muscle cells were resuspended in cold 1X PBS and fixed with 2% of formaldehyde at room temperature for 10 min. 0.2 M glycine was then added to stop fixation. Hi C: Hi C experiments on adult zebrafish brain and muscle tissues were performed according to previously published protocolRao et al.  2014. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 100 bp high throughput sequencing using HiSeq 2500  or HiSeq 4000Illumina. WGBS: Tübingen adult tissues were dissected  and the genomic DNA was extracted using DNeasy Blood & Tissue Kit Qiagen  69504. Then 1 µg of genomic DNA of each adult tissue was subjected to bisulfite conversion using EZ DNA Methylation Gold Kits WGBS: The final libraries were prepared using the Accel NGS® Methyl Seq DNA Library Kit. scATAC seq: Single cell ATAC seq scATAC seq was performed in one female brain and one male brain  respectively  on the 10X Genomics platform. To isolate nuclei  freshly dissected single brain was transferred to 1 mL NbActiv1 medium BrainBits  NbActiv1 500 with a wide bore pipette tip to break the tissue into small pieces. Then the tissue was broken up completely using regular bore pipette tips followed by filtering through a 30 µm cell strainer. The isolated cells were spun down at 500 g for 5 min at 4 °C and then lysed in 100 µL chilled 0.1X Lysis Buffer 10 mM Tris HCl  pH 7.5  10 mM NaCl  3 mM MgCl2  1% BSA 0.01% Tween 20  0.01% NP40 and 0.001% digitonin on ice for 5 min. Then 1 mL chilled Wash Buffer 10 mM Tris HCl  pH 7.5  10 mM NaCl  3 mM MgCl2  1% BSA  0.1% Tween 20 was added to the lysed cells and cells were spun down at 500 g for 5 min at 4 °C. At last  300 µL chilled Diluted Nuclei Buffer 10x Genomics  PN 2000153/2000207 was added to resuspend the nuclei. The nuclei were filtered again using a 30 µm cell strainer before cell counting scATAC seq: Around 12 000 nuclei were used for one Tn5 tagmentation reaction  and the scATAC seq library was prepared and sequenced exactly according to the company's user guide.,GEO Accession:GSM4662085,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP213938,,,YueLab-RNA-seq-Blood-rep1_1.fastq.gz YueLab-RNA-seq-Blood-rep1_2.fastq.gz,fastq fastq,10181340496.0,33713048.0,GSM4662085 r1,0:151 1:151,A:2735674306;C:2352790027;G:2376786768;T:2715986044;N:103351,151,151,,,2735674306,2352790027,2376786768,2715986044,103351,SRX8688332,SRS6966993,SRA919194,GEO,"Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine",2,0.91563,0.91373,0.11339,0.11315,0.82235,0.82266,0.48854,0.48669,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,sc,single_cell_droplet,10x,,United States,2020-07-08,Pharyngula,Embryo,Blood,Hematopoietic System
57171,SRR11243180,SRX7854786,SRS6264269,SRP251673,PRJNA610520,A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish,GSE146404,Transcriptome Analysis,To profile the developmental landscape of fetal HSPCs and their local niche  here  by using single cell RNA sequencing  we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10× Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study.,,pubmed:33785593,,4.5 dpf CHT cells,GSM4384818,,source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells,4.5 dpf CHT cells,UMI tools was used to analysis our single cell data.Firstly  in “whitelist” step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI  and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters  so that we can use STAR to map to the reference genome. Finally  in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples  measured by UMI counts,zebrafish embryos,,Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics  120237 following the manufacture’s introduction.,,genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells,GSM4384818,GSM4384818: 4.5 dpf CHT cells; Danio rerio; RNA Seq,GSM4384818,,1,Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics  120237 following the manufacture's introduction.,GEO Accession:GSM4384818,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP251673,,,171353H-CHT-4dpf_3_2_R1.fq.gz 171353H-CHT-4dpf_3_2_R2.fq.gz,fastq fastq,30131096700.0,100436989.0,GSM4384818 r1,0:150 1:150,A:6727746568;C:5761021689;G:10040248562;T:7601697440;N:382441,150,150,,,6727746568,5761021689,10040248562,7601697440,382441,SRX7854786,SRS6264269,SRA1051251,GEO,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.9175,0.0,0.06023,1.0,0.84208,,0.51614,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2020-03-05,Larval,Larval,Blood,Hematopoietic System
57172,SRR11243181,SRX7854786,SRS6264269,SRP251673,PRJNA610520,A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish,GSE146404,Transcriptome Analysis,To profile the developmental landscape of fetal HSPCs and their local niche  here  by using single cell RNA sequencing  we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10× Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study.,,pubmed:33785593,,4.5 dpf CHT cells,GSM4384818,,source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells,4.5 dpf CHT cells,UMI tools was used to analysis our single cell data.Firstly  in “whitelist” step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI  and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters  so that we can use STAR to map to the reference genome. Finally  in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples  measured by UMI counts,zebrafish embryos,,Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics  120237 following the manufacture’s introduction.,,genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells,GSM4384818,GSM4384818: 4.5 dpf CHT cells; Danio rerio; RNA Seq,GSM4384818,,1,Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics  120237 following the manufacture's introduction.,GEO Accession:GSM4384818,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP251673,,,171353H-CHT-4dpf_2-2_R1.fq.gz 171353H-CHT-4dpf_2-2_R2.fq.gz,fastq fastq,35454747300.0,118182491.0,GSM4384818 r2,0:150 1:150,A:7924515815;C:6769046954;G:11812021964;T:8948714749;N:447818,150,150,,,7924515815,6769046954,11812021964,8948714749,447818,SRX7854786,SRS6264269,SRA1051251,GEO,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.91808,0.0,0.05945,1.0,0.83938,,0.52604,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2020-03-05,Larval,Larval,Blood,Hematopoietic System
57173,SRR11243182,SRX7854786,SRS6264269,SRP251673,PRJNA610520,A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish,GSE146404,Transcriptome Analysis,To profile the developmental landscape of fetal HSPCs and their local niche  here  by using single cell RNA sequencing  we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10× Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study.,,pubmed:33785593,,4.5 dpf CHT cells,GSM4384818,,source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells,4.5 dpf CHT cells,UMI tools was used to analysis our single cell data.Firstly  in “whitelist” step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI  and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters  so that we can use STAR to map to the reference genome. Finally  in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples  measured by UMI counts,zebrafish embryos,,Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics  120237 following the manufacture’s introduction.,,genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells,GSM4384818,GSM4384818: 4.5 dpf CHT cells; Danio rerio; RNA Seq,GSM4384818,,1,Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics  120237 following the manufacture's introduction.,GEO Accession:GSM4384818,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP251673,,,171353H-CHT-4dpf_2_R1.fq.gz 171353H-CHT-4dpf_2_R2.fq.gz,fastq fastq,15872844300.0,52909481.0,GSM4384818 r3,0:150 1:150,A:3729663981;C:3022353413;G:5072752670;T:4047900723;N:173513,150,150,,,3729663981,3022353413,5072752670,4047900723,173513,SRX7854786,SRS6264269,SRA1051251,GEO,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.92013,0.0,0.0618,1.0,0.83871,,0.51823,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2020-03-05,Larval,Larval,Blood,Hematopoietic System
57174,SRR11243183,SRX7854786,SRS6264269,SRP251673,PRJNA610520,A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish,GSE146404,Transcriptome Analysis,To profile the developmental landscape of fetal HSPCs and their local niche  here  by using single cell RNA sequencing  we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10× Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study.,,pubmed:33785593,,4.5 dpf CHT cells,GSM4384818,,source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells,4.5 dpf CHT cells,UMI tools was used to analysis our single cell data.Firstly  in “whitelist” step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI  and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters  so that we can use STAR to map to the reference genome. Finally  in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples  measured by UMI counts,zebrafish embryos,,Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics  120237 following the manufacture’s introduction.,,genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells,GSM4384818,GSM4384818: 4.5 dpf CHT cells; Danio rerio; RNA Seq,GSM4384818,,1,Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics  120237 following the manufacture's introduction.,GEO Accession:GSM4384818,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP251673,,,171353H-CHT-4dpf_1_R1.fq.gz 171353H-CHT-4dpf_1_R2.fq.gz,fastq fastq,17996156400.0,59987188.0,GSM4384818 r4,0:150 1:150,A:4218380165;C:3448565478;G:5754713324;T:4574296718;N:200715,150,150,,,4218380165,3448565478,5754713324,4574296718,200715,SRX7854786,SRS6264269,SRA1051251,GEO,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.92379,0.0,0.06035,1.0,0.83857,,0.52292,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2020-03-05,Larval,Larval,Blood,Hematopoietic System
57175,SRR11243184,SRX7854786,SRS6264269,SRP251673,PRJNA610520,A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish,GSE146404,Transcriptome Analysis,To profile the developmental landscape of fetal HSPCs and their local niche  here  by using single cell RNA sequencing  we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10× Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study.,,pubmed:33785593,,4.5 dpf CHT cells,GSM4384818,,source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells,4.5 dpf CHT cells,UMI tools was used to analysis our single cell data.Firstly  in “whitelist” step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI  and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters  so that we can use STAR to map to the reference genome. Finally  in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples  measured by UMI counts,zebrafish embryos,,Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics  120237 following the manufacture’s introduction.,,genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells,GSM4384818,GSM4384818: 4.5 dpf CHT cells; Danio rerio; RNA Seq,GSM4384818,,1,Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics  120237 following the manufacture's introduction.,GEO Accession:GSM4384818,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP251673,,,171353H-CHT-4dpf_1-2_R1.fq.gz 171353H-CHT-4dpf_1-2_R2.fq.gz,fastq fastq,39542324700.0,131807749.0,GSM4384818 r5,0:150 1:150,A:8830009820;C:7582391853;G:13173552664;T:9955867355;N:503008,150,150,,,8830009820,7582391853,13173552664,9955867355,503008,SRX7854786,SRS6264269,SRA1051251,GEO,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.91925,0.0,0.05821,1.0,0.83989,,0.50837,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2020-03-05,Larval,Larval,Blood,Hematopoietic System
57176,SRR11243176,SRX7854785,SRS6264267,SRP251673,PRJNA610520,A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish,GSE146404,Transcriptome Analysis,To profile the developmental landscape of fetal HSPCs and their local niche  here  by using single cell RNA sequencing  we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10× Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study.,,pubmed:33785593,,3.5 dpf CHT cells,GSM4384817,,source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:3.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells,3.5 dpf CHT cells,UMI tools was used to analysis our single cell data.Firstly  in “whitelist” step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI  and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters  so that we can use STAR to map to the reference genome. Finally  in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples  measured by UMI counts,zebrafish embryos,,Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics  120237 following the manufacture’s introduction.,,genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:3.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells,GSM4384817,GSM4384817: 3.5 dpf CHT cells; Danio rerio; RNA Seq,GSM4384817,,1,Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics  120237 following the manufacture's introduction.,GEO Accession:GSM4384817,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP251673,,,171353F_CHT-3dpf_4_R1.fq.gz 171353F_CHT-3dpf_4_R2.fq.gz,fastq fastq,71692100700.0,238973669.0,GSM4384817 r1,0:150 1:150,A:17020567059;C:13566816873;G:21814800469;T:19287755240;N:2161059,150,150,,,17020567059,13566816873,21814800469,19287755240,2161059,SRX7854785,SRS6264267,SRA1051251,GEO,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.9088,0.0,0.06027,1.0,0.82733,,0.50573,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2020-03-05,Larval,Larval,Blood,Hematopoietic System
57177,SRR11243177,SRX7854785,SRS6264267,SRP251673,PRJNA610520,A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish,GSE146404,Transcriptome Analysis,To profile the developmental landscape of fetal HSPCs and their local niche  here  by using single cell RNA sequencing  we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10× Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study.,,pubmed:33785593,,3.5 dpf CHT cells,GSM4384817,,source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:3.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells,3.5 dpf CHT cells,UMI tools was used to analysis our single cell data.Firstly  in “whitelist” step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI  and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters  so that we can use STAR to map to the reference genome. Finally  in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples  measured by UMI counts,zebrafish embryos,,Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics  120237 following the manufacture’s introduction.,,genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:3.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells,GSM4384817,GSM4384817: 3.5 dpf CHT cells; Danio rerio; RNA Seq,GSM4384817,,1,Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics  120237 following the manufacture's introduction.,GEO Accession:GSM4384817,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP251673,,,171353F_CHT-3dpf_1_R2.fq.gz 171353F_CHT-3dpf_1_R1.fq.gz,fastq fastq,57793587900.0,192645293.0,GSM4384817 r2,0:150 1:150,A:13736253697;C:10912235777;G:17579141926;T:15564212842;N:1743658,150,150,,,13736253697,10912235777,17579141926,15564212842,1743658,SRX7854785,SRS6264267,SRA1051251,GEO,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.90774,0.0,0.06058,1.0,0.82875,,0.49524,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2020-03-05,Larval,Larval,Blood,Hematopoietic System
57178,SRR11243178,SRX7854785,SRS6264267,SRP251673,PRJNA610520,A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish,GSE146404,Transcriptome Analysis,To profile the developmental landscape of fetal HSPCs and their local niche  here  by using single cell RNA sequencing  we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10× Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study.,,pubmed:33785593,,3.5 dpf CHT cells,GSM4384817,,source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:3.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells,3.5 dpf CHT cells,UMI tools was used to analysis our single cell data.Firstly  in “whitelist” step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI  and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters  so that we can use STAR to map to the reference genome. Finally  in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples  measured by UMI counts,zebrafish embryos,,Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics  120237 following the manufacture’s introduction.,,genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:3.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells,GSM4384817,GSM4384817: 3.5 dpf CHT cells; Danio rerio; RNA Seq,GSM4384817,,1,Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics  120237 following the manufacture's introduction.,GEO Accession:GSM4384817,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP251673,,,171353F_CHT-3dpf_3_R2.fq.gz 171353F_CHT-3dpf_3_R1.fq.gz,fastq fastq,63713003700.0,212376679.0,GSM4384817 r3,0:150 1:150,A:15098662178;C:12078656688;G:19421188669;T:17112576360;N:1919805,150,150,,,15098662178,12078656688,19421188669,17112576360,1919805,SRX7854785,SRS6264267,SRA1051251,GEO,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.90945,0.0,0.06034,1.0,0.83149,,0.50559,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2020-03-05,Larval,Larval,Blood,Hematopoietic System
57179,SRR11243179,SRX7854785,SRS6264267,SRP251673,PRJNA610520,A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish,GSE146404,Transcriptome Analysis,To profile the developmental landscape of fetal HSPCs and their local niche  here  by using single cell RNA sequencing  we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10× Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study.,,pubmed:33785593,,3.5 dpf CHT cells,GSM4384817,,source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:3.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells,3.5 dpf CHT cells,UMI tools was used to analysis our single cell data.Firstly  in “whitelist” step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI  and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters  so that we can use STAR to map to the reference genome. Finally  in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples  measured by UMI counts,zebrafish embryos,,Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics  120237 following the manufacture’s introduction.,,genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:3.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells,GSM4384817,GSM4384817: 3.5 dpf CHT cells; Danio rerio; RNA Seq,GSM4384817,,1,Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics  120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen  37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics  120237 following the manufacture's introduction.,GEO Accession:GSM4384817,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP251673,,,171353F_CHT-3dpf_2_R1.fq.gz 171353F_CHT-3dpf_2_R2.fq.gz,fastq fastq,71620433400.0,238734778.0,GSM4384817 r4,0:150 1:150,A:16843285494;C:13823957864;G:21855431757;T:19095628638;N:2129647,150,150,,,16843285494,13823957864,21855431757,19095628638,2129647,SRX7854785,SRS6264267,SRA1051251,GEO,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.90995,0.0,0.06019,1.0,0.82767,,0.49515,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2020-03-05,Larval,Larval,Blood,Hematopoietic System
60923,SRR12658672,SRX9139730,SRS7381396,SRP282672,PRJNA663960,Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development,GSE158099,Transcriptome Analysis,We used single cell RNA sequencing to investigate the expression and the heterogeneity of wild type and runx1 mutant cd41 GFPLow cd41GFP hematopoietic stem and progenitor cells at embryonic 2.5 dpf  dpf and larval stages 6  10 dpf 16 dpf. Overall design: Single cell RNA seq with FACS sorted cd41 GFPlow cells from wild type and runx1 /  at 2.5  6  10 dpf 16 dpf.,parent bioproject:PRJNA663961,pubmed:34492681,,cd41:GFPlow runx1 /  bloodless 16dpf,GSM4792215,,tissue:sorted cd41:GFPlow|strain:EK|genotype/variation:runx1 /  del8  hg96 tgcd41:GFP|age:16 dpf|cell subset:sorted cd41:GFPlow,cd41:GFPlow runx1 /  bloodless 16dpf,Sequences from the Chromium platform were de multiplexed and aligned using CellRanger ver. 2.0.2 from 10x Genomics using custom zebrafish reference genome GRCz10 and transcript annotation reference GRCz10.87 with default parameters. Genome build: GRCz10 Supplementary files format and content: barcodes.tsv  genes.tsv  features.tsv  matrix.mtx,sorted cd41:GFPlow,,Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell 3’ Library & Gel Bead Kit v3. Cell lysis  cDNA preparation and library construction were prepared following the manufacturer's protocol.,,strain:EK|genotype/variation:runx1 /  del8  hg96 tgcd41:GFP|age:16 dpf|cell subset:sorted cd41:GFPlow,GSM4792215,GSM4792215: cd41:GFPlow runx1 /  bloodless 16dpf; Danio rerio; RNA Seq,GSM4792215,,1,Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell three prime Library & Gel Bead Kit v3. Cell lysis  cDNA preparation and library construction were prepared following the manufacturer's protocol.,GEO Accession:GSM4792215,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP282672,,loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=SC8.EB200211 2.R1.fastq.gz   read2PairFiles=SC8.EB200211 2.R2.fastq.gz   read3PairFiles=SC8.EB200211 2.I1.fastq.gz,SC8.EB200211_2.I1.fastq.gz SC8.EB200211_2.R1.fastq.gz SC8.EB200211_2.R2.fastq.gz,fastq fastq fastq,31985659032.0,238698948.0,GSM4792215 r1,0:28 1:98 2:8,A:8834796646;C:7245480386;G:7345360172;T:8558850270;N:1171558,28,98,8,,8834796646,7245480386,7345360172,8558850270,1171558,SRX9139730,SRS7381396,SRA1126726,GEO,NHGRI,1,0.93838,,0.0839,,0.7558,,0.51065,,98,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-09-16,Larval,Larval,Blood,Hematopoietic System
61983,SRR13080692,SRX9527457,SRS7734428,SRP293088,PRJNA679243,A Non Canonical Type 2 Immune Response Coordinates Tuberculous Granuloma Formation and Epithelialization,GSE161712,Other,Using the zebrafish M. marinum model  we identify the basis of granuloma macrophage transformation. Single cell RNA seq analysis of zebrafish granulomas as well as analysis of M. tuberculosis infected macaques reveal that  even in the presence of robust type 1 immune responses  countervailing type 2 signals associate with macrophage epithelialization. We find that type 2 immune signaling  mediated via stat6  is absolutely required for epithelialization and granuloma formation. Overall design: Wildtype zebrafish M. marinum granuloma single cell RNAseq profile.,,pubmed:33761328,,*AB wildtype zebrafish M.marinum granuloma cells,GSM4913139,,source name:WT Zebrafish granuloma cels|tissue:Granulomas|cell type:Granuloma cells|zebrafish strain:*AB,*AB wildtype zebrafish M.marinum granuloma cells,10X Cell Ranger was used to demultiplex raw base call BCL files generated by an Illumina sequencer into FASTQ before aligning them to the Ensembl zebrafish genome assembly GRCz11.96  performed filtering  barcode and UMI counting. Genome build: GRCz11.96 Supplementary files format and content: WTGran.matrix.mtx:  Gene barcode matrix in Market Exchange Format MEX for Mus musculus Uninjured Control & Injured1d  tibialis anterior muscle cells. Columns correspond to individual cellsbarcodes  while rows correspond to genes. Supplementary files format and content: WTGran.features.tsv: Genes corresponding to row indices in matrix.mtx. Gene ID and gene name are stored in the first and second column. Supplementary files format and content: WTGran.barcodes.tsv: Barcode sequences that correspond to column indices in matrix.mtx.,WT Zebrafish granuloma cels,,Granulomas were microdissected from of tissues 14 days post infection and cells dissociated using 30 minute incubation with 0.05% trypsin/EDTA Library preparation was done using Chromium Single Cell 3’ GEM  Library and Gel Bead Kit v3.,Adult  wildtype *AB zebrafish were infected with 350 fluorescent bacteria of M. marinum.,tissue:Granulomas|cell type:Granuloma cells|zebrafish strain:*AB,GSM4913139,GSM4913139: *AB wildtype zebrafish M.marinum granuloma cells; Danio rerio; RNA Seq,GSM4913139,,1,Granulomas were microdissected from of tissues 14 days post infection and cells dissociated using 30 minute incubation with 0.05% trypsin/EDTA Library preparation was done using Chromium Single Cell three prime GEM  Library and Gel Bead Kit v3.,GEO Accession:GSM4913139,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP293088,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=5761 S1 L001 I1 001.fastq.gz   read2PairFiles=5761 S1 L001 R1 001.fastq.gz   read3PairFiles=5761 S1 L001 R2 001.fastq.gz,5761_S1_L001_I1_001.fastq.gz 5761_S1_L001_R1_001.fastq.gz 5761_S1_L001_R2_001.fastq.gz,fastq fastq fastq,13295345266.0,104687758.0,GSM4913139 r1,0:8 1:28 2:91,A:3755348831;C:2900888340;G:2979576059;T:3656820253;N:2711783,8,28,91,,3755348831,2900888340,2979576059,3656820253,2711783,SRX9527457,SRS7734428,SRA1160946,GEO,"Tobin, Molecular Genetics and Microbiology, Duke University",1,0.92709,,0.13791,,0.81929,,0.57724,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-11-18,Adult,Adult,Blood,Hematopoietic System
61984,SRR13080693,SRX9527457,SRS7734428,SRP293088,PRJNA679243,A Non Canonical Type 2 Immune Response Coordinates Tuberculous Granuloma Formation and Epithelialization,GSE161712,Other,Using the zebrafish M. marinum model  we identify the basis of granuloma macrophage transformation. Single cell RNA seq analysis of zebrafish granulomas as well as analysis of M. tuberculosis infected macaques reveal that  even in the presence of robust type 1 immune responses  countervailing type 2 signals associate with macrophage epithelialization. We find that type 2 immune signaling  mediated via stat6  is absolutely required for epithelialization and granuloma formation. Overall design: Wildtype zebrafish M. marinum granuloma single cell RNAseq profile.,,pubmed:33761328,,*AB wildtype zebrafish M.marinum granuloma cells,GSM4913139,,source name:WT Zebrafish granuloma cels|tissue:Granulomas|cell type:Granuloma cells|zebrafish strain:*AB,*AB wildtype zebrafish M.marinum granuloma cells,10X Cell Ranger was used to demultiplex raw base call BCL files generated by an Illumina sequencer into FASTQ before aligning them to the Ensembl zebrafish genome assembly GRCz11.96  performed filtering  barcode and UMI counting. Genome build: GRCz11.96 Supplementary files format and content: WTGran.matrix.mtx:  Gene barcode matrix in Market Exchange Format MEX for Mus musculus Uninjured Control & Injured1d  tibialis anterior muscle cells. Columns correspond to individual cellsbarcodes  while rows correspond to genes. Supplementary files format and content: WTGran.features.tsv: Genes corresponding to row indices in matrix.mtx. Gene ID and gene name are stored in the first and second column. Supplementary files format and content: WTGran.barcodes.tsv: Barcode sequences that correspond to column indices in matrix.mtx.,WT Zebrafish granuloma cels,,Granulomas were microdissected from of tissues 14 days post infection and cells dissociated using 30 minute incubation with 0.05% trypsin/EDTA Library preparation was done using Chromium Single Cell 3’ GEM  Library and Gel Bead Kit v3.,Adult  wildtype *AB zebrafish were infected with 350 fluorescent bacteria of M. marinum.,tissue:Granulomas|cell type:Granuloma cells|zebrafish strain:*AB,GSM4913139,GSM4913139: *AB wildtype zebrafish M.marinum granuloma cells; Danio rerio; RNA Seq,GSM4913139,,1,Granulomas were microdissected from of tissues 14 days post infection and cells dissociated using 30 minute incubation with 0.05% trypsin/EDTA Library preparation was done using Chromium Single Cell three prime GEM  Library and Gel Bead Kit v3.,GEO Accession:GSM4913139,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP293088,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=5895 S1 L001 I1 001.fastq.gz   read2PairFiles=5895 S1 L001 R1 001.fastq.gz   read3PairFiles=5895 S1 L001 R2 001.fastq.gz,5895_S1_L001_I1_001.fastq.gz 5895_S1_L001_R1_001.fastq.gz 5895_S1_L001_R2_001.fastq.gz,fastq fastq fastq,17723636384.0,139556192.0,GSM4913139 r2,0:8 1:28 2:91,A:4955483447;C:3902218538;G:4036183306;T:4807856940;N:21894153,8,28,91,,4955483447,3902218538,4036183306,4807856940,21894153,SRX9527457,SRS7734428,SRA1160946,GEO,"Tobin, Molecular Genetics and Microbiology, Duke University",1,0.9176,,0.13304,,0.81462,,0.57616,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-11-18,Adult,Adult,Blood,Hematopoietic System
65651,SRR15483596,SRX11783413,SRS9786611,SRP332734,PRJNA755310,Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae,GSE182213,Transcriptome Analysis,The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.,,pubmed:34525360,,runx1:mCherry+ at 52 hpf #2 replicate,GSM5525118,,tissue:hematopoietic cells|developmental stage:52 hpf line:runx1+23:nls mCherry,runx1:mCherry+ at 52 hpf #2 replicate,Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities,hematopoietic cells,,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,,developmental stage:52 hpf line:runx1+23:nls mCherry,GSM5525118,GSM5525118: runx1:mCherry+ at 52 hpf #2 replicate; Danio rerio; RNA Seq,GSM5525118,,1,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,GEO Accession:GSM5525118,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP332734,,loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=R2 2 S1 L001 R1 001.fastq.gz   read2PairFiles=R2 2 S1 L001 R2 001.fastq.gz   read3PairFiles=R2 2 S1 L001 I1 001.fastq.gz,R2-2_S1_L001_I1_001.fastq.gz R2-2_S1_L001_R1_001.fastq.gz R2-2_S1_L001_R2_001.fastq.gz,fastq fastq fastq,59162946612.0,192087489.0,GSM5525118 r1,0:150 1:150 2:8,A:6826510360;C:7720741166;G:7033747534;T:7231279942;N:844348,150,150,8,,6826510360,7720741166,7033747534,7231279942,844348,SRX11783413,SRS9786611,SRA1278863,GEO,"Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine",1,0.95266,,0.01784,,0.93022,,0.46235,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-08-16,Hatching,Embryo,Blood,Hematopoietic System
65652,SRR15483597,SRX11783413,SRS9786611,SRP332734,PRJNA755310,Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae,GSE182213,Transcriptome Analysis,The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.,,pubmed:34525360,,runx1:mCherry+ at 52 hpf #2 replicate,GSM5525118,,tissue:hematopoietic cells|developmental stage:52 hpf line:runx1+23:nls mCherry,runx1:mCherry+ at 52 hpf #2 replicate,Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities,hematopoietic cells,,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,,developmental stage:52 hpf line:runx1+23:nls mCherry,GSM5525118,GSM5525118: runx1:mCherry+ at 52 hpf #2 replicate; Danio rerio; RNA Seq,GSM5525118,,1,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,GEO Accession:GSM5525118,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP332734,,loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=R2 2 S1 L002 R1 001.fastq.gz   read2PairFiles=R2 2 S1 L002 R2 001.fastq.gz   read3PairFiles=R2 2 S1 L002 I1 001.fastq.gz,R2-2_S1_L002_I1_001.fastq.gz R2-2_S1_L002_R1_001.fastq.gz R2-2_S1_L002_R2_001.fastq.gz,fastq fastq fastq,67940768588.0,220586911.0,GSM5525118 r2,0:150 1:150 2:8,A:7901205395;C:8819719149;G:8118311347;T:8243562587;N:5238172,150,150,8,,7901205395,8819719149,8118311347,8243562587,5238172,SRX11783413,SRS9786611,SRA1278863,GEO,"Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine",1,0.94536,,0.018,,0.92839,,0.45489,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-08-16,Hatching,Embryo,Blood,Hematopoietic System
65653,SRR15483594,SRX11783412,SRS9786609,SRP332734,PRJNA755310,Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae,GSE182213,Transcriptome Analysis,The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.,,pubmed:34525360,,runx1:mCherry+ at 52 hpf #1,GSM5525117,,tissue:hematopoietic cells|developmental stage:52 hpf line:runx1+23:nls mCherry,runx1:mCherry+ at 52 hpf #1,Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities,hematopoietic cells,,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,,developmental stage:52 hpf line:runx1+23:nls mCherry,GSM5525117,GSM5525117: runx1:mCherry+ at 52 hpf #1; Danio rerio; RNA Seq,GSM5525117,,1,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,GEO Accession:GSM5525117,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP332734,,loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=R2 1 S1 L001 R1 001.fastq.gz   read2PairFiles=R2 1 S1 L001 R2 001.fastq.gz   read3PairFiles=R2 1 S1 L001 I1 001.fastq.gz,R2-1_S1_L001_I1_001.fastq.gz R2-1_S1_L001_R1_001.fastq.gz R2-1_S1_L001_R2_001.fastq.gz,fastq fastq fastq,64542996056.0,209555182.0,GSM5525117 r1,0:150 1:150 2:8,A:7500200023;C:8401456631;G:7492567345;T:8038123819;N:929482,150,150,8,,7500200023,8401456631,7492567345,8038123819,929482,SRX11783412,SRS9786609,SRA1278863,GEO,"Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine",1,0.94027,,0.01204,,0.94107,,0.46801,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-08-16,Hatching,Embryo,Blood,Hematopoietic System
65654,SRR15483595,SRX11783412,SRS9786609,SRP332734,PRJNA755310,Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae,GSE182213,Transcriptome Analysis,The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.,,pubmed:34525360,,runx1:mCherry+ at 52 hpf #1,GSM5525117,,tissue:hematopoietic cells|developmental stage:52 hpf line:runx1+23:nls mCherry,runx1:mCherry+ at 52 hpf #1,Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities,hematopoietic cells,,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,,developmental stage:52 hpf line:runx1+23:nls mCherry,GSM5525117,GSM5525117: runx1:mCherry+ at 52 hpf #1; Danio rerio; RNA Seq,GSM5525117,,1,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,GEO Accession:GSM5525117,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP332734,,loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=R2 1 S1 L002 R1 001.fastq.gz   read2PairFiles=R2 1 S1 L002 R2 001.fastq.gz   read3PairFiles=R2 1 S1 L002 I1 001.fastq.gz,R2-1_S1_L002_I1_001.fastq.gz R2-1_S1_L002_R1_001.fastq.gz R2-1_S1_L002_R2_001.fastq.gz,fastq fastq fastq,61129147772.0,198471259.0,GSM5525117 r2,0:150 1:150 2:8,A:7164346674;C:7911114850;G:7135136885;T:7555336618;N:4753823,150,150,8,,7164346674,7911114850,7135136885,7555336618,4753823,SRX11783412,SRS9786609,SRA1278863,GEO,"Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine",1,0.93152,,0.01164,,0.94152,,0.46255,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-08-16,Hatching,Embryo,Blood,Hematopoietic System
65655,SRR15483588,SRX11783411,SRS9786608,SRP332734,PRJNA755310,Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae,GSE182213,Transcriptome Analysis,The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.,,pubmed:34525360,,draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate,GSM5525116,,tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate,Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities,hematopoietic cells,,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,,developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,GSM5525116,GSM5525116: draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate; Danio rerio; RNA Seq,GSM5525116,,1,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,GEO Accession:GSM5525116,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP332734,,loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=DG2 2 S1 L001 R1 001.fastq.gz   read2PairFiles=DG2 2 S1 L001 R2 001.fastq.gz   read3PairFiles=DG2 2 S1 L001 I1 001.fastq.gz,DG2-2_S1_L001_I1_001.fastq.gz DG2-2_S1_L001_R1_001.fastq.gz DG2-2_S1_L001_R2_001.fastq.gz,fastq fastq fastq,58062154920.0,188513490.0,GSM5525116 r1,0:150 1:150 2:8,A:6786904201;C:7461082970;G:6741279762;T:7286929534;N:827033,150,150,8,,6786904201,7461082970,6741279762,7286929534,827033,SRX11783411,SRS9786608,SRA1278863,GEO,"Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine",1,0.9442,,0.02532,,0.92577,,0.45185,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-08-16,Hatching,Embryo,Blood,Hematopoietic System
65656,SRR15483589,SRX11783411,SRS9786608,SRP332734,PRJNA755310,Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae,GSE182213,Transcriptome Analysis,The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.,,pubmed:34525360,,draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate,GSM5525116,,tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate,Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities,hematopoietic cells,,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,,developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,GSM5525116,GSM5525116: draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate; Danio rerio; RNA Seq,GSM5525116,,1,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,GEO Accession:GSM5525116,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP332734,,loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=DG2 2 S1 L002 R1 001.fastq.gz   read2PairFiles=DG2 2 S1 L002 R2 001.fastq.gz   read3PairFiles=DG2 2 S1 L002 I1 001.fastq.gz,DG2-2_S1_L002_I1_001.fastq.gz DG2-2_S1_L002_R1_001.fastq.gz DG2-2_S1_L002_R2_001.fastq.gz,fastq fastq fastq,71629010068.0,232561721.0,GSM5525116 r2,0:150 1:150 2:8,A:8422157482;C:9164931651;G:8346143692;T:8946552575;N:4472750,150,150,8,,8422157482,9164931651,8346143692,8946552575,4472750,SRX11783411,SRS9786608,SRA1278863,GEO,"Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine",1,0.93666,,0.02678,,0.92232,,0.44942,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-08-16,Hatching,Embryo,Blood,Hematopoietic System
65657,SRR15483590,SRX11783411,SRS9786608,SRP332734,PRJNA755310,Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae,GSE182213,Transcriptome Analysis,The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.,,pubmed:34525360,,draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate,GSM5525116,,tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate,Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities,hematopoietic cells,,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,,developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,GSM5525116,GSM5525116: draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate; Danio rerio; RNA Seq,GSM5525116,,1,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,GEO Accession:GSM5525116,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP332734,,,DG2-2_S1_L003_R1_001.fastq.gz DG2-2_S1_L003_R2_001.fastq.gz,fastq fastq,32047702200.0,106825674.0,GSM5525116 r3,0:150 1:150,A:7309683350;C:6236246000;G:6254785333;T:12244316725;N:2670792,150,150,,,7309683350,6236246000,6254785333,12244316725,2670792,SRX11783411,SRS9786608,SRA1278863,GEO,"Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine",2,0.01831,0.94417,0.00206,0.02463,0.99691,0.92423,0.53203,0.45728,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-08-16,Hatching,Embryo,Blood,Hematopoietic System
65658,SRR15483591,SRX11783411,SRS9786608,SRP332734,PRJNA755310,Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae,GSE182213,Transcriptome Analysis,The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.,,pubmed:34525360,,draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate,GSM5525116,,tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate,Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities,hematopoietic cells,,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,,developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,GSM5525116,GSM5525116: draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate; Danio rerio; RNA Seq,GSM5525116,,1,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,GEO Accession:GSM5525116,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP332734,,,DG2-2_S1_L004_R1_001.fastq.gz DG2-2_S1_L004_R2_001.fastq.gz,fastq fastq,37463959500.0,124879865.0,GSM5525116 r4,0:150 1:150,A:8552446843;C:7287672885;G:7301637904;T:14319175980;N:3025888,150,150,,,8552446843,7287672885,7301637904,14319175980,3025888,SRX11783411,SRS9786608,SRA1278863,GEO,"Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine",2,0.0179,0.94533,0.00191,0.0243,0.99691,0.92261,0.49722,0.45421,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-08-16,Hatching,Embryo,Blood,Hematopoietic System
65659,SRR15483592,SRX11783411,SRS9786608,SRP332734,PRJNA755310,Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae,GSE182213,Transcriptome Analysis,The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.,,pubmed:34525360,,draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate,GSM5525116,,tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate,Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities,hematopoietic cells,,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,,developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,GSM5525116,GSM5525116: draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate; Danio rerio; RNA Seq,GSM5525116,,1,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,GEO Accession:GSM5525116,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP332734,,,DG2-2_S1_L005_R1_001.fastq.gz DG2-2_S1_L005_R2_001.fastq.gz,fastq fastq,30981057900.0,103270193.0,GSM5525116 r5,0:150 1:150,A:7076201480;C:6026934261;G:6065200560;T:11810111130;N:2610469,150,150,,,7076201480,6026934261,6065200560,11810111130,2610469,SRX11783411,SRS9786608,SRA1278863,GEO,"Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine",2,0.01658,0.93855,0.00198,0.02394,0.99734,0.92476,0.53823,0.45548,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-08-16,Hatching,Embryo,Blood,Hematopoietic System
65660,SRR15483593,SRX11783411,SRS9786608,SRP332734,PRJNA755310,Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae,GSE182213,Transcriptome Analysis,The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.,,pubmed:34525360,,draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate,GSM5525116,,tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate,Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities,hematopoietic cells,,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,,developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,GSM5525116,GSM5525116: draculin:mCherry+;gata1:GFP  at 52 hpf #2 replicate; Danio rerio; RNA Seq,GSM5525116,,1,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,GEO Accession:GSM5525116,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP332734,,,DG2-2_S1_L006_R1_001.fastq.gz DG2-2_S1_L006_R2_001.fastq.gz,fastq fastq,33497811000.0,111659370.0,GSM5525116 r6,0:150 1:150,A:7673047524;C:6494998239;G:6520425795;T:12806463581;N:2875861,150,150,,,7673047524,6494998239,6520425795,12806463581,2875861,SRX11783411,SRS9786608,SRA1278863,GEO,"Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine",2,0.01712,0.94074,0.00206,0.02516,0.99701,0.92318,0.56268,0.45333,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-08-16,Hatching,Embryo,Blood,Hematopoietic System
65661,SRR15483582,SRX11783410,SRS9786606,SRP332734,PRJNA755310,Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae,GSE182213,Transcriptome Analysis,The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.,,pubmed:34525360,,draculin:mCherry+;gata1:GFP  at 52 hpf #1,GSM5525115,,tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,draculin:mCherry+;gata1:GFP  at 52 hpf #1,Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities,hematopoietic cells,,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,,developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,GSM5525115,GSM5525115: draculin:mCherry+;gata1:GFP  at 52 hpf #1; Danio rerio; RNA Seq,GSM5525115,,1,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,GEO Accession:GSM5525115,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP332734,,loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=DG2 1 S1 L001 R1 001.fastq.gz   read2PairFiles=DG2 1 S1 L001 R2 001.fastq.gz   read3PairFiles=DG2 1 S1 L001 I1 001.fastq.gz,DG2-1_S1_L001_I1_001.fastq.gz DG2-1_S1_L001_R1_001.fastq.gz DG2-1_S1_L001_R2_001.fastq.gz,fastq fastq fastq,53816019796.0,174727337.0,GSM5525115 r1,0:150 1:150 2:8,A:6268319263;C:6935405810;G:6236287882;T:6768309909;N:777686,150,150,8,,6268319263,6935405810,6236287882,6768309909,777686,SRX11783410,SRS9786606,SRA1278863,GEO,"Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine",1,0.94373,,0.02418,,0.93206,,0.4538,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-08-16,Hatching,Embryo,Blood,Hematopoietic System
65662,SRR15483583,SRX11783410,SRS9786606,SRP332734,PRJNA755310,Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae,GSE182213,Transcriptome Analysis,The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.,,pubmed:34525360,,draculin:mCherry+;gata1:GFP  at 52 hpf #1,GSM5525115,,tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,draculin:mCherry+;gata1:GFP  at 52 hpf #1,Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities,hematopoietic cells,,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,,developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,GSM5525115,GSM5525115: draculin:mCherry+;gata1:GFP  at 52 hpf #1; Danio rerio; RNA Seq,GSM5525115,,1,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,GEO Accession:GSM5525115,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP332734,,loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=DG2 1 S1 L002 R1 001.fastq.gz   read2PairFiles=DG2 1 S1 L002 R2 001.fastq.gz   read3PairFiles=DG2 1 S1 L002 I1 001.fastq.gz,DG2-1_S1_L002_I1_001.fastq.gz DG2-1_S1_L002_R1_001.fastq.gz DG2-1_S1_L002_R2_001.fastq.gz,fastq fastq fastq,56656687472.0,183950284.0,GSM5525115 r2,0:150 1:150 2:8,A:6636746214;C:7271043747;G:6588518102;T:7092648593;N:3585944,150,150,8,,6636746214,7271043747,6588518102,7092648593,3585944,SRX11783410,SRS9786606,SRA1278863,GEO,"Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine",1,0.9348,,0.02385,,0.93156,,0.45273,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-08-16,Hatching,Embryo,Blood,Hematopoietic System
65663,SRR15483584,SRX11783410,SRS9786606,SRP332734,PRJNA755310,Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae,GSE182213,Transcriptome Analysis,The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.,,pubmed:34525360,,draculin:mCherry+;gata1:GFP  at 52 hpf #1,GSM5525115,,tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,draculin:mCherry+;gata1:GFP  at 52 hpf #1,Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities,hematopoietic cells,,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,,developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,GSM5525115,GSM5525115: draculin:mCherry+;gata1:GFP  at 52 hpf #1; Danio rerio; RNA Seq,GSM5525115,,1,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,GEO Accession:GSM5525115,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP332734,,,DG2-1_S1_L003_R1_001.fastq.gz DG2-1_S1_L003_R2_001.fastq.gz,fastq fastq,33218500800.0,110728336.0,GSM5525115 r3,0:150 1:150,A:7550847416;C:6408594085;G:6405597564;T:12826295610;N:27166125,150,150,,,7550847416,6408594085,6405597564,12826295610,27166125,SRX11783410,SRS9786606,SRA1278863,GEO,"Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine",2,0.02176,0.94163,0.00286,0.02347,0.99703,0.92991,0.46265,0.45574,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-08-16,Hatching,Embryo,Blood,Hematopoietic System
65664,SRR15483585,SRX11783410,SRS9786606,SRP332734,PRJNA755310,Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae,GSE182213,Transcriptome Analysis,The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.,,pubmed:34525360,,draculin:mCherry+;gata1:GFP  at 52 hpf #1,GSM5525115,,tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,draculin:mCherry+;gata1:GFP  at 52 hpf #1,Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities,hematopoietic cells,,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,,developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,GSM5525115,GSM5525115: draculin:mCherry+;gata1:GFP  at 52 hpf #1; Danio rerio; RNA Seq,GSM5525115,,1,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,GEO Accession:GSM5525115,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP332734,,,DG2-1_S1_L004_R1_001.fastq.gz DG2-1_S1_L004_R2_001.fastq.gz,fastq fastq,33634915800.0,112116386.0,GSM5525115 r4,0:150 1:150,A:7645827173;C:6494042604;G:6493405590;T:12974094595;N:27545838,150,150,,,7645827173,6494042604,6493405590,12974094595,27545838,SRX11783410,SRS9786606,SRA1278863,GEO,"Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine",2,0.02104,0.9407,0.00263,0.02247,0.99701,0.93257,0.49246,0.4561,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-08-16,Hatching,Embryo,Blood,Hematopoietic System
65665,SRR15483586,SRX11783410,SRS9786606,SRP332734,PRJNA755310,Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae,GSE182213,Transcriptome Analysis,The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.,,pubmed:34525360,,draculin:mCherry+;gata1:GFP  at 52 hpf #1,GSM5525115,,tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,draculin:mCherry+;gata1:GFP  at 52 hpf #1,Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities,hematopoietic cells,,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,,developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,GSM5525115,GSM5525115: draculin:mCherry+;gata1:GFP  at 52 hpf #1; Danio rerio; RNA Seq,GSM5525115,,1,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,GEO Accession:GSM5525115,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP332734,,,DG2-1_S1_L005_R1_001.fastq.gz DG2-1_S1_L005_R2_001.fastq.gz,fastq fastq,34113860700.0,113712869.0,GSM5525115 r5,0:150 1:150,A:7749471214;C:6598363925;G:6596788535;T:13141319294;N:27917732,150,150,,,7749471214,6598363925,6596788535,13141319294,27917732,SRX11783410,SRS9786606,SRA1278863,GEO,"Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine",2,0.02131,0.94056,0.0023,0.02334,0.99719,0.93164,0.50985,0.45474,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-08-16,Hatching,Embryo,Blood,Hematopoietic System
65666,SRR15483587,SRX11783410,SRS9786606,SRP332734,PRJNA755310,Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae,GSE182213,Transcriptome Analysis,The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.,,pubmed:34525360,,draculin:mCherry+;gata1:GFP  at 52 hpf #1,GSM5525115,,tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,draculin:mCherry+;gata1:GFP  at 52 hpf #1,Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities,hematopoietic cells,,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,,developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,GSM5525115,GSM5525115: draculin:mCherry+;gata1:GFP  at 52 hpf #1; Danio rerio; RNA Seq,GSM5525115,,1,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,GEO Accession:GSM5525115,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP332734,,,DG2-1_S1_L006_R1_001.fastq.gz DG2-1_S1_L006_R2_001.fastq.gz,fastq fastq,34597356600.0,115324522.0,GSM5525115 r6,0:150 1:150,A:7866654210;C:6690644103;G:6695640643;T:13316020558;N:28397086,150,150,,,7866654210,6690644103,6695640643,13316020558,28397086,SRX11783410,SRS9786606,SRA1278863,GEO,"Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine",2,0.02131,0.94082,0.00235,0.02244,0.99665,0.93089,0.53827,0.45518,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-08-16,Hatching,Embryo,Blood,Hematopoietic System
65667,SRR15483581,SRX11783409,SRS9786607,SRP332734,PRJNA755310,Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae,GSE182213,Transcriptome Analysis,The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.,,pubmed:34525360,,draculin:mCherry+;gata1:GFP  at 30 hpf #2 replicate,GSM5525114,,tissue:hematopoietic cells|developmental stage:30 hpf line:draculin:mCherry;gata1:GFP,draculin:mCherry+;gata1:GFP  at 30 hpf #2 replicate,Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities,hematopoietic cells,,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,,developmental stage:30 hpf line:draculin:mCherry;gata1:GFP,GSM5525114,GSM5525114: draculin:mCherry+;gata1:GFP  at 30 hpf #2 replicate; Danio rerio; RNA Seq,GSM5525114,,1,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,GEO Accession:GSM5525114,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP332734,,loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=DG1 3 S1 L001 R1 001.fastq.gz   read2PairFiles=DG1 3 S1 L001 R2 001.fastq.gz   read3PairFiles=DG1 3 S1 L001 I1 001.fastq.gz,DG1-3_S1_L001_I1_001.fastq.gz DG1-3_S1_L001_R1_001.fastq.gz DG1-3_S1_L001_R2_001.fastq.gz,fastq fastq fastq,53654080172.0,174201559.0,GSM5525114 r1,0:150 1:150 2:8,A:6842604916;C:6327854414;G:6203934909;T:6755061460;N:778151,150,150,8,,6842604916,6327854414,6203934909,6755061460,778151,SRX11783409,SRS9786607,SRA1278863,GEO,"Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine",1,0.92988,,0.06632,,0.84691,,0.45741,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-08-16,Pharyngula,Embryo,Blood,Hematopoietic System
65668,SRR15483580,SRX11783408,SRS9786605,SRP332734,PRJNA755310,Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae,GSE182213,Transcriptome Analysis,The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf  using Illumina HiSeq. Samples conducted in replicate.,,pubmed:34525360,,draculin:mCherry+;gata1:GFP  at 30 hpf #1,GSM5525113,,tissue:hematopoietic cells|developmental stage:30 hpf line:draculin:mCherry;gata1:GFP,draculin:mCherry+;gata1:GFP  at 30 hpf #1,Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment  filtering  barcode counting  and unique molecular identifier counting. Filtered outputs from cell ranger features  barcodes  and matrix were analyzed using Seurat V4 Hao et al.  2020 and Monocle 3 Trapnell et al.  2014; Cao et al.  2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al.  2018. scVelo Bergen et al.  2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities,hematopoietic cells,,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,,developmental stage:30 hpf line:draculin:mCherry;gata1:GFP,GSM5525113,GSM5525113: draculin:mCherry+;gata1:GFP  at 30 hpf #1; Danio rerio; RNA Seq,GSM5525113,,1,draculin:mCherry+;gata1:GFP  or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using  Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al.  2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.,GEO Accession:GSM5525113,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP332734,,loader:fastq load.py|options:  platform=Illumina   readTypes=TBT   read1PairFiles=DG1 2 S1 L001 R1 001.fastq.gz   read2PairFiles=DG1 2 S1 L001 R2 001.fastq.gz   read3PairFiles=DG1 2 S1 L001 I1 001.fastq.gz,DG1-2_S1_L001_I1_001.fastq.gz DG1-2_S1_L001_R1_001.fastq.gz DG1-2_S1_L001_R2_001.fastq.gz,fastq fastq fastq,65514487192.0,212709374.0,GSM5525113 r1,0:150 1:150 2:8,A:8050271487;C:8057897221;G:7684156435;T:8113136954;N:944003,150,150,8,,8050271487,8057897221,7684156435,8113136954,944003,SRX11783408,SRS9786605,SRA1278863,GEO,"Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine",1,0.94401,,0.03521,,0.88339,,0.35428,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-08-16,Pharyngula,Embryo,Blood,Hematopoietic System
70833,SRR20668414,SRX16690958,SRS14321723,SRP388388,PRJNA862882,An anti inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish,GSE209884,Transcriptome Analysis,Single cell RNA sequencing on FACS sorted cells from the zebrafish macrophage in 5df embryos in 11 different samples: homeo  15min neomycin  1hr post neo  3hr post neo  5hr post neo  il10ra sib homeo  il10ra sib 1hr  il10ra sib 3hr  il10ra mut homeo  il10ra mut 1hr and  il10ra mut 3hr Overall design: scRNA seq,,pubmed:36127326,,3hr il10ra mut homozygous/mutant,GSM6404047,,source name:macrophage|age:5dpf|tissue:macrophage|genotype:3hr il10ra mut homozygous/mutant|strain:Tgmpeg:GFP,3hr il10ra mut homozygous/mutant,Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10  ensembl release 91  using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Assembly: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.,macrophage,,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,age:5dpf|tissue:macrophage|genotype:3hr il10ra mut homozygous/mutant|strain:Tgmpeg:GFP,GSM6404047,GSM6404047: 3hr il10ra mut homozygous/mutant; Danio rerio; RNA Seq,GSM6404047 r1,GSM6404047,1,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP388388,,intentional duplicate|dangling references:treat as unmapped,3h_il10ra_mut_possorted_genome_bam.bam,10X Genomics bam file,62119485701.0,682631711.0,GSM6404047 r1,0:91,A:19063458673;C:12969646294;G:14996142121;T:15088275965;N:1962648,91,,,,19063458673,12969646294,14996142121,15088275965,1962648,SRX16690958,SRS14321723,SRA1469295,Stowers institute for medical research,Stowers institute for medical research,1,0.90083,,0.13953,,0.81852,,0.58114,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-07-27,Larval,Larval,Blood,Hematopoietic System
70834,SRR20668415,SRX16690957,SRS14321722,SRP388388,PRJNA862882,An anti inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish,GSE209884,Transcriptome Analysis,Single cell RNA sequencing on FACS sorted cells from the zebrafish macrophage in 5df embryos in 11 different samples: homeo  15min neomycin  1hr post neo  3hr post neo  5hr post neo  il10ra sib homeo  il10ra sib 1hr  il10ra sib 3hr  il10ra mut homeo  il10ra mut 1hr and  il10ra mut 3hr Overall design: scRNA seq,,pubmed:36127326,,1hr il10ra mut homozygous/mutant,GSM6404046,,source name:macrophage|age:5dpf|tissue:macrophage|genotype:1hr il10ra mut homozygous/mutant|strain:Tgmpeg:GFP,1hr il10ra mut homozygous/mutant,Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10  ensembl release 91  using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Assembly: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.,macrophage,,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,age:5dpf|tissue:macrophage|genotype:1hr il10ra mut homozygous/mutant|strain:Tgmpeg:GFP,GSM6404046,GSM6404046: 1hr il10ra mut homozygous/mutant; Danio rerio; RNA Seq,GSM6404046 r1,GSM6404046,1,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP388388,,intentional duplicate|dangling references:treat as unmapped,1h_il10ra_mut_possorted_genome_bam.bam,10X Genomics bam file,53760457023.0,590774253.0,GSM6404046 r1,0:91,A:16112436932;C:11497272850;G:13478420835;T:12670631386;N:1695020,91,,,,16112436932,11497272850,13478420835,12670631386,1695020,SRX16690957,SRS14321722,SRA1469295,Stowers institute for medical research,Stowers institute for medical research,1,0.88181,,0.15256,,0.84642,,0.59854,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-07-27,Larval,Larval,Blood,Hematopoietic System
70835,SRR20668416,SRX16690956,SRS14321721,SRP388388,PRJNA862882,An anti inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish,GSE209884,Transcriptome Analysis,Single cell RNA sequencing on FACS sorted cells from the zebrafish macrophage in 5df embryos in 11 different samples: homeo  15min neomycin  1hr post neo  3hr post neo  5hr post neo  il10ra sib homeo  il10ra sib 1hr  il10ra sib 3hr  il10ra mut homeo  il10ra mut 1hr and  il10ra mut 3hr Overall design: scRNA seq,,pubmed:36127326,,homeo il10ra mut homozygous/mutant,GSM6404045,,source name:macrophage|age:5dpf|tissue:macrophage|genotype:homeo il10ra mut homozygous/mutant|strain:Tgmpeg:GFP,homeo il10ra mut homozygous/mutant,Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10  ensembl release 91  using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Assembly: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.,macrophage,,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,age:5dpf|tissue:macrophage|genotype:homeo il10ra mut homozygous/mutant|strain:Tgmpeg:GFP,GSM6404045,GSM6404045: homeo il10ra mut homozygous/mutant; Danio rerio; RNA Seq,GSM6404045 r1,GSM6404045,1,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP388388,,intentional duplicate|dangling references:treat as unmapped,homeo_il10ra_mut_possorted_genome_bam.bam,10X Genomics bam file,54884218571.0,603123281.0,GSM6404045 r1,0:91,A:16107511497;C:11798904382;G:12911246344;T:14064824012;N:1732336,91,,,,16107511497,11798904382,12911246344,14064824012,1732336,SRX16690956,SRS14321721,SRA1469295,Stowers institute for medical research,Stowers institute for medical research,1,0.92347,,0.15847,,0.80762,,0.4962,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-07-27,Larval,Larval,Blood,Hematopoietic System
70836,SRR20668417,SRX16690955,SRS14321720,SRP388388,PRJNA862882,An anti inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish,GSE209884,Transcriptome Analysis,Single cell RNA sequencing on FACS sorted cells from the zebrafish macrophage in 5df embryos in 11 different samples: homeo  15min neomycin  1hr post neo  3hr post neo  5hr post neo  il10ra sib homeo  il10ra sib 1hr  il10ra sib 3hr  il10ra mut homeo  il10ra mut 1hr and  il10ra mut 3hr Overall design: scRNA seq,,pubmed:36127326,,3hr il10ra sib heterozygous/sibling,GSM6404044,,source name:macrophage|age:5dpf|tissue:macrophage|genotype:3hr il10ra sib heterozygous/sibling|strain:Tgmpeg:GFP,3hr il10ra sib heterozygous/sibling,Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10  ensembl release 91  using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Assembly: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.,macrophage,,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,age:5dpf|tissue:macrophage|genotype:3hr il10ra sib heterozygous/sibling|strain:Tgmpeg:GFP,GSM6404044,GSM6404044: 3hr il10ra sib heterozygous/sibling; Danio rerio; RNA Seq,GSM6404044 r1,GSM6404044,1,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP388388,,intentional duplicate|dangling references:treat as unmapped,3h_il10ra_sib_possorted_genome_bam.bam,10X Genomics bam file,76164218312.0,836969432.0,GSM6404044 r1,0:91,A:24495666579;C:15379395913;G:18054974511;T:18231782170;N:2399139,91,,,,24495666579,15379395913,18054974511,18231782170,2399139,SRX16690955,SRS14321720,SRA1469295,Stowers institute for medical research,Stowers institute for medical research,1,0.8984,,0.13627,,0.8254,,0.5844,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-07-27,Larval,Larval,Blood,Hematopoietic System
70837,SRR20668418,SRX16690954,SRS14321718,SRP388388,PRJNA862882,An anti inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish,GSE209884,Transcriptome Analysis,Single cell RNA sequencing on FACS sorted cells from the zebrafish macrophage in 5df embryos in 11 different samples: homeo  15min neomycin  1hr post neo  3hr post neo  5hr post neo  il10ra sib homeo  il10ra sib 1hr  il10ra sib 3hr  il10ra mut homeo  il10ra mut 1hr and  il10ra mut 3hr Overall design: scRNA seq,,pubmed:36127326,,1hr il10ra sib heterozygous/sibling,GSM6404043,,source name:macrophage|age:5dpf|tissue:macrophage|genotype:1hr il10ra sib heterozygous/sibling|strain:Tgmpeg:GFP,1hr il10ra sib heterozygous/sibling,Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10  ensembl release 91  using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Assembly: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.,macrophage,,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,age:5dpf|tissue:macrophage|genotype:1hr il10ra sib heterozygous/sibling|strain:Tgmpeg:GFP,GSM6404043,GSM6404043: 1hr il10ra sib heterozygous/sibling; Danio rerio; RNA Seq,GSM6404043 r1,GSM6404043,1,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP388388,,intentional duplicate|dangling references:treat as unmapped,1h_il10ra_sib_possorted_genome_bam.bam,10X Genomics bam file,55980175069.0,615166759.0,GSM6404043 r1,0:91,A:17214450499;C:11610450029;G:13903261037;T:13250244220;N:1769284,91,,,,17214450499,11610450029,13903261037,13250244220,1769284,SRX16690954,SRS14321718,SRA1469295,Stowers institute for medical research,Stowers institute for medical research,1,0.86967,,0.1721,,0.84147,,0.6182,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-07-27,Larval,Larval,Blood,Hematopoietic System
70838,SRR20668419,SRX16690953,SRS14321719,SRP388388,PRJNA862882,An anti inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish,GSE209884,Transcriptome Analysis,Single cell RNA sequencing on FACS sorted cells from the zebrafish macrophage in 5df embryos in 11 different samples: homeo  15min neomycin  1hr post neo  3hr post neo  5hr post neo  il10ra sib homeo  il10ra sib 1hr  il10ra sib 3hr  il10ra mut homeo  il10ra mut 1hr and  il10ra mut 3hr Overall design: scRNA seq,,pubmed:36127326,,homeo il10ra sib heterozygous/sibling,GSM6404042,,source name:macrophage|age:5dpf|tissue:macrophage|genotype:homeo il10ra sib heterozygous/sibling|strain:Tgmpeg:GFP,homeo il10ra sib heterozygous/sibling,Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10  ensembl release 91  using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Assembly: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.,macrophage,,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,age:5dpf|tissue:macrophage|genotype:homeo il10ra sib heterozygous/sibling|strain:Tgmpeg:GFP,GSM6404042,GSM6404042: homeo il10ra sib heterozygous/sibling; Danio rerio; RNA Seq,GSM6404042 r1,GSM6404042,1,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP388388,,intentional duplicate|dangling references:treat as unmapped,homeo_il10ra_sib_possorted_genome_bam.bam,10X Genomics bam file,65823260594.0,723332534.0,GSM6404042 r1,0:91,A:19277950772;C:14136710715;G:15444723963;T:16961801916;N:2073228,91,,,,19277950772,14136710715,15444723963,16961801916,2073228,SRX16690953,SRS14321719,SRA1469295,Stowers institute for medical research,Stowers institute for medical research,1,0.92472,,0.14491,,0.8103,,0.56302,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-07-27,Larval,Larval,Blood,Hematopoietic System
70839,SRR20668420,SRX16690952,SRS14321717,SRP388388,PRJNA862882,An anti inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish,GSE209884,Transcriptome Analysis,Single cell RNA sequencing on FACS sorted cells from the zebrafish macrophage in 5df embryos in 11 different samples: homeo  15min neomycin  1hr post neo  3hr post neo  5hr post neo  il10ra sib homeo  il10ra sib 1hr  il10ra sib 3hr  il10ra mut homeo  il10ra mut 1hr and  il10ra mut 3hr Overall design: scRNA seq,,pubmed:36127326,,5hr post neomycin,GSM6404041,,source name:macrophage|age:5dpf|tissue:macrophage|genotype:5hr post neomycin|strain:Tgmpeg:GFP,5hr post neomycin,Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10  ensembl release 91  using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Assembly: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.,macrophage,,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,age:5dpf|tissue:macrophage|genotype:5hr post neomycin|strain:Tgmpeg:GFP,GSM6404041,GSM6404041: 5hr post neomycin; Danio rerio; RNA Seq,GSM6404041 r1,GSM6404041,1,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP388388,,assembly:danRer10|intentional duplicate|dangling references:treat as unmapped,5hr_possorted_genome_bam.bam,10X Genomics bam file,35604069046.0,391253506.0,GSM6404041 r1,0:91,A:10384029234;C:7578909209;G:8255823659;T:9384782607;N:524337,91,,,,10384029234,7578909209,8255823659,9384782607,524337,SRX16690952,SRS14321717,SRA1469295,Stowers institute for medical research,Stowers institute for medical research,1,0.93723,,0.11988,,0.80541,,0.54155,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-07-27,Larval,Larval,Blood,Hematopoietic System
70840,SRR20668421,SRX16690951,SRS14321716,SRP388388,PRJNA862882,An anti inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish,GSE209884,Transcriptome Analysis,Single cell RNA sequencing on FACS sorted cells from the zebrafish macrophage in 5df embryos in 11 different samples: homeo  15min neomycin  1hr post neo  3hr post neo  5hr post neo  il10ra sib homeo  il10ra sib 1hr  il10ra sib 3hr  il10ra mut homeo  il10ra mut 1hr and  il10ra mut 3hr Overall design: scRNA seq,,pubmed:36127326,,3hr post neomycin,GSM6404040,,source name:macrophage|age:5dpf|tissue:macrophage|genotype:3hr post neomycin|strain:Tgmpeg:GFP,3hr post neomycin,Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10  ensembl release 91  using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Assembly: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.,macrophage,,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,age:5dpf|tissue:macrophage|genotype:3hr post neomycin|strain:Tgmpeg:GFP,GSM6404040,GSM6404040: 3hr post neomycin; Danio rerio; RNA Seq,GSM6404040 r1,GSM6404040,1,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP388388,,assembly:danRer10|intentional duplicate|dangling references:treat as unmapped,3h_possorted_genome_bam.bam,10X Genomics bam file,33149245584.0,364277424.0,GSM6404040 r1,0:91,A:9699362543;C:7042480303;G:7729260559;T:8677650345;N:491834,91,,,,9699362543,7042480303,7729260559,8677650345,491834,SRX16690951,SRS14321716,SRA1469295,Stowers institute for medical research,Stowers institute for medical research,1,0.93611,,0.12582,,0.80476,,0.53981,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-07-27,Larval,Larval,Blood,Hematopoietic System
70841,SRR20668422,SRX16690950,SRS14321715,SRP388388,PRJNA862882,An anti inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish,GSE209884,Transcriptome Analysis,Single cell RNA sequencing on FACS sorted cells from the zebrafish macrophage in 5df embryos in 11 different samples: homeo  15min neomycin  1hr post neo  3hr post neo  5hr post neo  il10ra sib homeo  il10ra sib 1hr  il10ra sib 3hr  il10ra mut homeo  il10ra mut 1hr and  il10ra mut 3hr Overall design: scRNA seq,,pubmed:36127326,,1hr post neomycin,GSM6404039,,source name:macrophage|age:5dpf|tissue:macrophage|genotype:1hr post neomycin|strain:Tgmpeg:GFP,1hr post neomycin,Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10  ensembl release 91  using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Assembly: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.,macrophage,,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,age:5dpf|tissue:macrophage|genotype:1hr post neomycin|strain:Tgmpeg:GFP,GSM6404039,GSM6404039: 1hr post neomycin; Danio rerio; RNA Seq,GSM6404039 r1,GSM6404039,1,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP388388,,assembly:danRer10|intentional duplicate|dangling references:treat as unmapped,1hr_possorted_genome_bam.bam,10X Genomics bam file,31569863871.0,346921581.0,GSM6404039 r1,0:91,A:9269126254;C:6667515682;G:7316895497;T:8315860639;N:465799,91,,,,9269126254,6667515682,7316895497,8315860639,465799,SRX16690950,SRS14321715,SRA1469295,Stowers institute for medical research,Stowers institute for medical research,1,0.93105,,0.12507,,0.81677,,0.52209,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-07-27,Larval,Larval,Blood,Hematopoietic System
70842,SRR20668423,SRX16690949,SRS14321714,SRP388388,PRJNA862882,An anti inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish,GSE209884,Transcriptome Analysis,Single cell RNA sequencing on FACS sorted cells from the zebrafish macrophage in 5df embryos in 11 different samples: homeo  15min neomycin  1hr post neo  3hr post neo  5hr post neo  il10ra sib homeo  il10ra sib 1hr  il10ra sib 3hr  il10ra mut homeo  il10ra mut 1hr and  il10ra mut 3hr Overall design: scRNA seq,,pubmed:36127326,,15min post neomycin,GSM6404038,,source name:macrophage|age:5dpf|tissue:macrophage|genotype:15min post neomycin|strain:Tgmpeg:GFP,15min post neomycin,Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10  ensembl release 91  using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Assembly: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.,macrophage,,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,age:5dpf|tissue:macrophage|genotype:15min post neomycin|strain:Tgmpeg:GFP,GSM6404038,GSM6404038: 15min post neomycin; Danio rerio; RNA Seq,GSM6404038 r1,GSM6404038,1,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP388388,,assembly:danRer10|intentional duplicate,15min_possorted_genome_bam.bam,10X Genomics bam file,31511277963.0,318295737.0,GSM6404038 r1,0:99,A:9298906016;C:6733626243;G:7314474144;T:8157192656;N:7078904,99,,,,9298906016,6733626243,7314474144,8157192656,7078904,SRX16690949,SRS14321714,SRA1469295,Stowers institute for medical research,Stowers institute for medical research,1,0.92846,,0.11694,,0.82055,,0.52675,,99,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-07-27,Larval,Larval,Blood,Hematopoietic System
70843,SRR20668424,SRX16690948,SRS14321713,SRP388388,PRJNA862882,An anti inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish,GSE209884,Transcriptome Analysis,Single cell RNA sequencing on FACS sorted cells from the zebrafish macrophage in 5df embryos in 11 different samples: homeo  15min neomycin  1hr post neo  3hr post neo  5hr post neo  il10ra sib homeo  il10ra sib 1hr  il10ra sib 3hr  il10ra mut homeo  il10ra mut 1hr and  il10ra mut 3hr Overall design: scRNA seq,,pubmed:36127326,,homeo,GSM6404037,,source name:macrophage|age:5dpf|tissue:macrophage|genotype:homeo|strain:Tgmpeg:GFP,homeo,Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome GRCz10  ensembl release 91  using the Cell Ranger version 2.1.1 pipeline from 10x genomics using the default settings. Assembly: danRer10 Supplementary files format and content: h5 files contain the UMI counts for each cell.,macrophage,,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,age:5dpf|tissue:macrophage|genotype:homeo|strain:Tgmpeg:GFP,GSM6404037,GSM6404037: homeo; Danio rerio; RNA Seq,GSM6404037 r1,GSM6404037,1,Presumptive macrophages GFP+ were isolated by FACS. Standard 10x genomics scRNA seq protocol using v3 chemistry,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP388388,,assembly:danRer10|intentional duplicate,homeo_possorted_genome_bam.bam,10X Genomics bam file,14120576910.0,142632090.0,GSM6404037 r1,0:99,A:4214242258;C:2942873461;G:3198194603;T:3761817001;N:3449587,99,,,,4214242258,2942873461,3198194603,3761817001,3449587,SRX16690948,SRS14321713,SRA1469295,Stowers institute for medical research,Stowers institute for medical research,1,0.91899,,0.15518,,0.81659,,0.54276,,99,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-07-27,Larval,Larval,Blood,Hematopoietic System