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 15009,ERR12306826,ERX11683773,ERS17043893,ERP155237,PRJEB70303,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E-MTAB-13554,Transcriptome Analysis,To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule but containing a detection fluorophores. post treatment the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,,Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,Coated,SAMEA114641726,KIS,ENA first public:2024 09 30|External Id:SAMEA114641726|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Coated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Coated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1,,,,,,,,,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E MTAB 13554:Coated p,Coated p,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,NextSeq 550,,ERP155237,NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,230324-Coated_S1_L003_I1_001.fastq.gz 230324-Coated_S1_L003_I2_001.fastq.gz 230324-Coated_S1_L003_R1_001.fastq.gz 230324-Coated_S1_L003_R2_001.fastq.gz,fastq fastq fastq fastq,10050750400.0,62817190.0,E MTAB 13554:230324 Coated S1 L003,0:10 1:10 2:30 3:110,A:1894211982;C:1556769050;G:1595134885;T:1863244619;N:530364,10,10,30,110,1894211982,1556769050,1595134885,1863244619,530364,ERX11683773,ERS17043893,ERA27417303,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-11-20,Hatching,Embryo,Whole Organism,All anatomical structures 15010,ERR12306829,ERX11683773,ERS17043893,ERP155237,PRJEB70303,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E-MTAB-13554,Transcriptome Analysis,To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule but containing a detection fluorophores. post treatment the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,,Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,Coated,SAMEA114641726,KIS,ENA first public:2024 09 30|External Id:SAMEA114641726|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Coated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Coated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1,,,,,,,,,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E MTAB 13554:Coated p,Coated p,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,NextSeq 550,,ERP155237,NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,230324-Coated_S1_L004_I1_001.fastq.gz 230324-Coated_S1_L004_I2_001.fastq.gz 230324-Coated_S1_L004_R1_001.fastq.gz 230324-Coated_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq,9780757760.0,61129736.0,E MTAB 13554:230324 Coated S1 L004,0:10 1:10 2:30 3:110,A:1844808667;C:1516149264;G:1549838165;T:1813091860;N:383004,10,10,30,110,1844808667,1516149264,1549838165,1813091860,383004,ERX11683773,ERS17043893,ERA27417303,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-11-20,Hatching,Embryo,Whole Organism,All anatomical structures 15011,ERR12306828,ERX11683773,ERS17043893,ERP155237,PRJEB70303,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E-MTAB-13554,Transcriptome Analysis,To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule but containing a detection fluorophores. post treatment the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,,Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,Coated,SAMEA114641726,KIS,ENA first public:2024 09 30|External Id:SAMEA114641726|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Coated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Coated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1,,,,,,,,,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E MTAB 13554:Coated p,Coated p,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,NextSeq 550,,ERP155237,NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,230324-Coated_S1_L002_I1_001.fastq.gz 230324-Coated_S1_L002_I2_001.fastq.gz 230324-Coated_S1_L002_R1_001.fastq.gz 230324-Coated_S1_L002_R2_001.fastq.gz,fastq fastq fastq fastq,9639368480.0,60246053.0,E MTAB 13554:230324 Coated S1 L002,0:10 1:10 2:30 3:110,A:1817388578;C:1494319441;G:1527564319;T:1787447672;N:345820,10,10,30,110,1817388578,1494319441,1527564319,1787447672,345820,ERX11683773,ERS17043893,ERA27417303,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-11-20,Hatching,Embryo,Whole Organism,All anatomical structures 15012,ERR12306832,ERX11683773,ERS17043893,ERP155237,PRJEB70303,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E-MTAB-13554,Transcriptome Analysis,To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule but containing a detection fluorophores. post treatment the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,,Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,Coated,SAMEA114641726,KIS,ENA first public:2024 09 30|External Id:SAMEA114641726|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Coated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Coated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1,,,,,,,,,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E MTAB 13554:Coated p,Coated p,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,NextSeq 550,,ERP155237,NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,230324-Coated_S1_L001_I1_001.fastq.gz 230324-Coated_S1_L001_I2_001.fastq.gz 230324-Coated_S1_L001_R1_001.fastq.gz 230324-Coated_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,9823147840.0,61394674.0,E MTAB 13554:230324 Coated S1 L001,0:10 1:10 2:30 3:110,A:1851113558;C:1521671335;G:1558230628;T:1822067428;N:331191,10,10,30,110,1851113558,1521671335,1558230628,1822067428,331191,ERX11683773,ERS17043893,ERA27417303,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-11-20,Hatching,Embryo,Whole Organism,All anatomical structures 15013,ERR12306833,ERX11683774,ERS17043894,ERP155237,PRJEB70303,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E-MTAB-13554,Transcriptome Analysis,To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule but containing a detection fluorophores. post treatment the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,,Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,Uncoated,SAMEA114641727,KIS,ENA first public:2024 09 30|External Id:SAMEA114641727|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Uncoated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Uncoated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1,,,,,,,,,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E MTAB 13554:Uncoated p,Uncoated p,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,NextSeq 550,,ERP155237,NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,230324-Uncoated_S2_L001_I1_001.fastq.gz 230324-Uncoated_S2_L001_I2_001.fastq.gz 230324-Uncoated_S2_L001_R1_001.fastq.gz 230324-Uncoated_S2_L001_R2_001.fastq.gz,fastq fastq fastq fastq,8871716800.0,55448230.0,E MTAB 13554:230324 Uncoated S2 L001,0:10 1:10 2:30 3:110,A:1718985845;C:1319560520;G:1372197713;T:1688254655;N:306567,10,10,30,110,1718985845,1319560520,1372197713,1688254655,306567,ERX11683774,ERS17043894,ERA27417303,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-11-20,Hatching,Embryo,Whole Organism,All anatomical structures 15014,ERR12306830,ERX11683774,ERS17043894,ERP155237,PRJEB70303,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E-MTAB-13554,Transcriptome Analysis,To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule but containing a detection fluorophores. post treatment the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,,Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,Uncoated,SAMEA114641727,KIS,ENA first public:2024 09 30|External Id:SAMEA114641727|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Uncoated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Uncoated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1,,,,,,,,,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E MTAB 13554:Uncoated p,Uncoated p,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,NextSeq 550,,ERP155237,NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,230324-Uncoated_S2_L003_I1_001.fastq.gz 230324-Uncoated_S2_L003_I2_001.fastq.gz 230324-Uncoated_S2_L003_R1_001.fastq.gz 230324-Uncoated_S2_L003_R2_001.fastq.gz,fastq fastq fastq fastq,9075478720.0,56721742.0,E MTAB 13554:230324 Uncoated S2 L003,0:10 1:10 2:30 3:110,A:1758677834;C:1349774831;G:1404463433;T:1725994897;N:480625,10,10,30,110,1758677834,1349774831,1404463433,1725994897,480625,ERX11683774,ERS17043894,ERA27417303,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-11-20,Hatching,Embryo,Whole Organism,All anatomical structures 15015,ERR12306831,ERX11683774,ERS17043894,ERP155237,PRJEB70303,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E-MTAB-13554,Transcriptome Analysis,To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule but containing a detection fluorophores. post treatment the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,,Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,Uncoated,SAMEA114641727,KIS,ENA first public:2024 09 30|External Id:SAMEA114641727|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Uncoated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Uncoated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1,,,,,,,,,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E MTAB 13554:Uncoated p,Uncoated p,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,NextSeq 550,,ERP155237,NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,230324-Uncoated_S2_L002_I1_001.fastq.gz 230324-Uncoated_S2_L002_I2_001.fastq.gz 230324-Uncoated_S2_L002_R1_001.fastq.gz 230324-Uncoated_S2_L002_R2_001.fastq.gz,fastq fastq fastq fastq,8705210880.0,54407568.0,E MTAB 13554:230324 Uncoated S2 L002,0:10 1:10 2:30 3:110,A:1687330583;C:1295837902;G:1345522657;T:1655826422;N:314916,10,10,30,110,1687330583,1295837902,1345522657,1655826422,314916,ERX11683774,ERS17043894,ERA27417303,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-11-20,Hatching,Embryo,Whole Organism,All anatomical structures 15016,ERR12306827,ERX11683774,ERS17043894,ERP155237,PRJEB70303,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E-MTAB-13554,Transcriptome Analysis,To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule but containing a detection fluorophores. post treatment the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,,Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,Uncoated,SAMEA114641727,KIS,ENA first public:2024 09 30|External Id:SAMEA114641727|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Uncoated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Uncoated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1,,,,,,,,,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E MTAB 13554:Uncoated p,Uncoated p,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,NextSeq 550,,ERP155237,NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,230324-Uncoated_S2_L004_I1_001.fastq.gz 230324-Uncoated_S2_L004_I2_001.fastq.gz 230324-Uncoated_S2_L004_R1_001.fastq.gz 230324-Uncoated_S2_L004_R2_001.fastq.gz,fastq fastq fastq fastq,8846203360.0,55288771.0,E MTAB 13554:230324 Uncoated S2 L004,0:10 1:10 2:30 3:110,A:1715100047;C:1316853239;G:1367208350;T:1682248092;N:355082,10,10,30,110,1715100047,1316853239,1367208350,1682248092,355082,ERX11683774,ERS17043894,ERA27417303,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-11-20,Hatching,Embryo,Whole Organism,All anatomical structures 24656,SRR25491963,SRX21223193,SRS18479996,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE cut replicate S12,GSM7676118,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE cut replicate S12,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676118,GSM7676118: KBTRE cut replicate S12; Danio rerio; RNA Seq,GSM7676118 r1,GSM7676118,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTREcut_S12_L001_R2_001.fastq.gz H27K5BCX2_KBTREcut_S12_L001_R1_001.fastq.gz H27K5BCX2_KBTREcut_S12_L001_I1_001.fastq.gz,fastq fastq fastq,664936140.0,5037395.0,GSM7676118 r1,0:8 1:26 2:98,A:143407233;C:100996340;G:110567290;T:138539687;N:154160,8,26,98,,143407233,100996340,110567290,138539687,154160,SRX21223193,SRS18479996,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91249,,0.11469,,0.85372,,0.50388,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24657,SRR25491964,SRX21223193,SRS18479996,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE cut replicate S12,GSM7676118,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE cut replicate S12,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676118,GSM7676118: KBTRE cut replicate S12; Danio rerio; RNA Seq,GSM7676118 r1,GSM7676118,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTREcut_S12_L001_R2_001.fastq.gz HFJ5GBCX2_KBTREcut_S12_L001_R1_001.fastq.gz HFJ5GBCX2_KBTREcut_S12_L001_I1_001.fastq.gz,fastq fastq fastq,645128748.0,4887339.0,GSM7676118 r2,0:8 1:26 2:98,A:139238913;C:98013961;G:107274566;T:134050699;N:381083,8,26,98,,139238913,98013961,107274566,134050699,381083,SRX21223193,SRS18479996,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91125,,0.11373,,0.85226,,0.50246,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24658,SRR25491965,SRX21223193,SRS18479996,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE cut replicate S12,GSM7676118,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE cut replicate S12,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676118,GSM7676118: KBTRE cut replicate S12; Danio rerio; RNA Seq,GSM7676118 r1,GSM7676118,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTREcut_S12_L001_I1_001.fastq.gz HYLGMBCXY_KBTREcut_S12_L001_R1_001.fastq.gz HYLGMBCXY_KBTREcut_S12_L001_R2_001.fastq.gz,fastq fastq fastq,701173044.0,5311917.0,GSM7676118 r3,0:8 1:26 2:98,A:151296425;C:106327416;G:116370981;T:144230427;N:2342617,8,26,98,,151296425,106327416,116370981,144230427,2342617,SRX21223193,SRS18479996,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91082,,0.11168,,0.85245,,0.5097,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24659,SRR25491966,SRX21223193,SRS18479996,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE cut replicate S12,GSM7676118,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE cut replicate S12,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676118,GSM7676118: KBTRE cut replicate S12; Danio rerio; RNA Seq,GSM7676118 r1,GSM7676118,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTREcut_S12_L001_I1_001.fastq.gz HYWGVBCXY_KBTREcut_S12_L001_R1_001.fastq.gz HYWGVBCXY_KBTREcut_S12_L001_R2_001.fastq.gz,fastq fastq fastq,656204604.0,4971247.0,GSM7676118 r4,0:8 1:26 2:98,A:141756368;C:99522317;G:109015686;T:136785011;N:102824,8,26,98,,141756368,99522317,109015686,136785011,102824,SRX21223193,SRS18479996,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.90953,,0.11383,,0.85212,,0.49917,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24660,SRR25492087,SRX21223193,SRS18479996,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE cut replicate S12,GSM7676118,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE cut replicate S12,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676118,GSM7676118: KBTRE cut replicate S12; Danio rerio; RNA Seq,GSM7676118 r1,GSM7676118,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTREcut_S12_L002_I1_001.fastq.gz H27K5BCX2_KBTREcut_S12_L002_R1_001.fastq.gz H27K5BCX2_KBTREcut_S12_L002_R2_001.fastq.gz,fastq fastq fastq,658691616.0,4990088.0,GSM7676118 r5,0:8 1:26 2:98,A:142071317;C:100089239;G:109564812;T:137176685;N:126571,8,26,98,,142071317,100089239,109564812,137176685,126571,SRX21223193,SRS18479996,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.9118,,0.11359,,0.85307,,0.49119,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24661,SRR25492088,SRX21223193,SRS18479996,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE cut replicate S12,GSM7676118,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE cut replicate S12,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676118,GSM7676118: KBTRE cut replicate S12; Danio rerio; RNA Seq,GSM7676118 r1,GSM7676118,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTREcut_S12_L002_I1_001.fastq.gz HFJ5GBCX2_KBTREcut_S12_L002_R1_001.fastq.gz HFJ5GBCX2_KBTREcut_S12_L002_R2_001.fastq.gz,fastq fastq fastq,626035872.0,4742696.0,GSM7676118 r6,0:8 1:26 2:98,A:135079818;C:95138940;G:104158101;T:130050700;N:356649,8,26,98,,135079818,95138940,104158101,130050700,356649,SRX21223193,SRS18479996,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.9103,,0.11494,,0.85378,,0.48986,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24662,SRR25492089,SRX21223193,SRS18479996,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE cut replicate S12,GSM7676118,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE cut replicate S12,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676118,GSM7676118: KBTRE cut replicate S12; Danio rerio; RNA Seq,GSM7676118 r1,GSM7676118,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTREcut_S12_L002_I1_001.fastq.gz HYLGMBCXY_KBTREcut_S12_L002_R1_001.fastq.gz HYLGMBCXY_KBTREcut_S12_L002_R2_001.fastq.gz,fastq fastq fastq,693479028.0,5253629.0,GSM7676118 r7,0:8 1:26 2:98,A:149676332;C:105134718;G:115079858;T:142696573;N:2268161,8,26,98,,149676332,105134718,115079858,142696573,2268161,SRX21223193,SRS18479996,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91107,,0.11027,,0.85354,,0.50421,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24663,SRR25492090,SRX21223193,SRS18479996,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE cut replicate S12,GSM7676118,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE cut replicate S12,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676118,GSM7676118: KBTRE cut replicate S12; Danio rerio; RNA Seq,GSM7676118 r1,GSM7676118,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTREcut_S12_L002_R2_001.fastq.gz HYWGVBCXY_KBTREcut_S12_L002_R1_001.fastq.gz HYWGVBCXY_KBTREcut_S12_L002_I1_001.fastq.gz,fastq fastq fastq,656957664.0,4976952.0,GSM7676118 r8,0:8 1:26 2:98,A:141922523;C:99627529;G:109167065;T:136992486;N:31693,8,26,98,,141922523,99627529,109167065,136992486,31693,SRX21223193,SRS18479996,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91107,,0.11379,,0.85346,,0.50695,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24664,SRR25491967,SRX21223192,SRS18479995,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE cut replicate S10,GSM7676116,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE cut replicate S10,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676116,GSM7676116: KBTRE cut replicate S10; Danio rerio; RNA Seq,GSM7676116 r1,GSM7676116,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTREcut_S10_L001_R2_001.fastq.gz H27K5BCX2_KBTREcut_S10_L001_R1_001.fastq.gz H27K5BCX2_KBTREcut_S10_L001_I1_001.fastq.gz,fastq fastq fastq,1062185256.0,8046858.0,GSM7676116 r1,0:8 1:26 2:98,A:230014489;C:161623855;G:176773666;T:219935294;N:244780,8,26,98,,230014489,161623855,176773666,219935294,244780,SRX21223192,SRS18479995,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91294,,0.11493,,0.85719,,0.50794,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24665,SRR25491968,SRX21223192,SRS18479995,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE cut replicate S10,GSM7676116,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE cut replicate S10,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676116,GSM7676116: KBTRE cut replicate S10; Danio rerio; RNA Seq,GSM7676116 r1,GSM7676116,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTREcut_S10_L001_R2_001.fastq.gz HFJ5GBCX2_KBTREcut_S10_L001_R1_001.fastq.gz HFJ5GBCX2_KBTREcut_S10_L001_I1_001.fastq.gz,fastq fastq fastq,1034539308.0,7837419.0,GSM7676116 r2,0:8 1:26 2:98,A:224616171;C:157304961;G:172084243;T:213455656;N:606031,8,26,98,,224616171,157304961,172084243,213455656,606031,SRX21223192,SRS18479995,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91287,,0.11588,,0.85415,,0.50804,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24666,SRR25491969,SRX21223192,SRS18479995,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE cut replicate S10,GSM7676116,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE cut replicate S10,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676116,GSM7676116: KBTRE cut replicate S10; Danio rerio; RNA Seq,GSM7676116 r1,GSM7676116,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTREcut_S10_L001_R2_001.fastq.gz HYLGMBCXY_KBTREcut_S10_L001_R1_001.fastq.gz HYLGMBCXY_KBTREcut_S10_L001_I1_001.fastq.gz,fastq fastq fastq,1122858660.0,8506505.0,GSM7676116 r3,0:8 1:26 2:98,A:243355100;C:170483208;G:186449194;T:229601473;N:3748515,8,26,98,,243355100,170483208,186449194,229601473,3748515,SRX21223192,SRS18479995,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91213,,0.11262,,0.8561,,0.49742,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24667,SRR25491970,SRX21223192,SRS18479995,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE cut replicate S10,GSM7676116,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE cut replicate S10,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676116,GSM7676116: KBTRE cut replicate S10; Danio rerio; RNA Seq,GSM7676116 r1,GSM7676116,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTREcut_S10_L001_I1_001.fastq.gz HYWGVBCXY_KBTREcut_S10_L001_R1_001.fastq.gz HYWGVBCXY_KBTREcut_S10_L001_R2_001.fastq.gz,fastq fastq fastq,1044506496.0,7912928.0,GSM7676116 r4,0:8 1:26 2:98,A:226413586;C:158757664;G:173768785;T:216364905;N:162004,8,26,98,,226413586,158757664,173768785,216364905,162004,SRX21223192,SRS18479995,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.9121,,0.11332,,0.85401,,0.51062,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24668,SRR25491971,SRX21223192,SRS18479995,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE cut replicate S10,GSM7676116,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE cut replicate S10,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676116,GSM7676116: KBTRE cut replicate S10; Danio rerio; RNA Seq,GSM7676116 r1,GSM7676116,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTREcut_S10_L002_I1_001.fastq.gz HYLGMBCXY_KBTREcut_S10_L002_R1_001.fastq.gz HYLGMBCXY_KBTREcut_S10_L002_R2_001.fastq.gz,fastq fastq fastq,1110246720.0,8410960.0,GSM7676116 r7,0:8 1:26 2:98,A:240787456;C:168521971;G:184254856;T:227029149;N:3680648,8,26,98,,240787456,168521971,184254856,227029149,3680648,SRX21223192,SRS18479995,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91246,,0.11301,,0.85449,,0.50422,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24669,SRR25491972,SRX21223192,SRS18479995,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE cut replicate S10,GSM7676116,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE cut replicate S10,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676116,GSM7676116: KBTRE cut replicate S10; Danio rerio; RNA Seq,GSM7676116 r1,GSM7676116,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTREcut_S10_L002_I1_001.fastq.gz HYWGVBCXY_KBTREcut_S10_L002_R1_001.fastq.gz HYWGVBCXY_KBTREcut_S10_L002_R2_001.fastq.gz,fastq fastq fastq,1046026740.0,7924445.0,GSM7676116 r8,0:8 1:26 2:98,A:226911006;C:158976256;G:173939936;T:216718492;N:49920,8,26,98,,226911006,158976256,173939936,216718492,49920,SRX21223192,SRS18479995,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91267,,0.11377,,0.8548,,0.50065,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24670,SRR25491989,SRX21223192,SRS18479995,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE cut replicate S10,GSM7676116,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE cut replicate S10,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676116,GSM7676116: KBTRE cut replicate S10; Danio rerio; RNA Seq,GSM7676116 r1,GSM7676116,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTREcut_S10_L002_I1_001.fastq.gz H27K5BCX2_KBTREcut_S10_L002_R1_001.fastq.gz H27K5BCX2_KBTREcut_S10_L002_R2_001.fastq.gz,fastq fastq fastq,1052457252.0,7973161.0,GSM7676116 r5,0:8 1:26 2:98,A:227727118;C:160159228;G:175278732;T:218004542;N:200158,8,26,98,,227727118,160159228,175278732,218004542,200158,SRX21223192,SRS18479995,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91307,,0.11551,,0.85634,,0.50392,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24671,SRR25491990,SRX21223192,SRS18479995,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE cut replicate S10,GSM7676116,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE cut replicate S10,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676116,GSM7676116: KBTRE cut replicate S10; Danio rerio; RNA Seq,GSM7676116 r1,GSM7676116,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTREcut_S10_L002_I1_001.fastq.gz HFJ5GBCX2_KBTREcut_S10_L002_R1_001.fastq.gz HFJ5GBCX2_KBTREcut_S10_L002_R2_001.fastq.gz,fastq fastq fastq,1003744500.0,7604125.0,GSM7676116 r6,0:8 1:26 2:98,A:217741909;C:152712224;G:167110758;T:207073522;N:565837,8,26,98,,217741909,152712224,167110758,207073522,565837,SRX21223192,SRS18479995,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91357,,0.11506,,0.85504,,0.49763,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24672,SRR25491973,SRX21223191,SRS18479994,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE cut replicate S11,GSM7676117,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE cut replicate S11,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676117,GSM7676117: KBTRE cut replicate S11; Danio rerio; RNA Seq,GSM7676117 r1,GSM7676117,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTREcut_S11_L001_I1_001.fastq.gz H27K5BCX2_KBTREcut_S11_L001_R1_001.fastq.gz H27K5BCX2_KBTREcut_S11_L001_R2_001.fastq.gz,fastq fastq fastq,927688740.0,7027945.0,GSM7676117 r1,0:8 1:26 2:98,A:200105466;C:141029173;G:154321296;T:193068023;N:214652,8,26,98,,200105466,141029173,154321296,193068023,214652,SRX21223191,SRS18479994,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91282,,0.1155,,0.85283,,0.5061,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24673,SRR25491974,SRX21223191,SRS18479994,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE cut replicate S11,GSM7676117,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE cut replicate S11,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676117,GSM7676117: KBTRE cut replicate S11; Danio rerio; RNA Seq,GSM7676117 r1,GSM7676117,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTREcut_S11_L001_R2_001.fastq.gz HFJ5GBCX2_KBTREcut_S11_L001_R1_001.fastq.gz HFJ5GBCX2_KBTREcut_S11_L001_I1_001.fastq.gz,fastq fastq fastq,897789420.0,6801435.0,GSM7676117 r2,0:8 1:26 2:98,A:193853631;C:136435624;G:149320255;T:186400739;N:530381,8,26,98,,193853631,136435624,149320255,186400739,530381,SRX21223191,SRS18479994,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91186,,0.11485,,0.85429,,0.49592,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24674,SRR25491975,SRX21223191,SRS18479994,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE cut replicate S11,GSM7676117,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE cut replicate S11,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676117,GSM7676117: KBTRE cut replicate S11; Danio rerio; RNA Seq,GSM7676117 r1,GSM7676117,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTREcut_S11_L001_R2_001.fastq.gz HYLGMBCXY_KBTREcut_S11_L001_R1_001.fastq.gz HYLGMBCXY_KBTREcut_S11_L001_I1_001.fastq.gz,fastq fastq fastq,978294372.0,7411321.0,GSM7676117 r3,0:8 1:26 2:98,A:211132117;C:148425540;G:162317813;T:201164320;N:3269668,8,26,98,,211132117,148425540,162317813,201164320,3269668,SRX21223191,SRS18479994,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91073,,0.1132,,0.8537,,0.50609,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24675,SRR25491976,SRX21223191,SRS18479994,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE cut replicate S11,GSM7676117,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE cut replicate S11,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676117,GSM7676117: KBTRE cut replicate S11; Danio rerio; RNA Seq,GSM7676117 r1,GSM7676117,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTREcut_S11_L001_I1_001.fastq.gz HYWGVBCXY_KBTREcut_S11_L001_R1_001.fastq.gz HYWGVBCXY_KBTREcut_S11_L001_R2_001.fastq.gz,fastq fastq fastq,918264996.0,6956553.0,GSM7676117 r4,0:8 1:26 2:98,A:198352554;C:139394187;G:152576773;T:191275437;N:143243,8,26,98,,198352554,139394187,152576773,191275437,143243,SRX21223191,SRS18479994,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91014,,0.1139,,0.85307,,0.50536,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24676,SRR25491977,SRX21223191,SRS18479994,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE cut replicate S11,GSM7676117,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE cut replicate S11,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676117,GSM7676117: KBTRE cut replicate S11; Danio rerio; RNA Seq,GSM7676117 r1,GSM7676117,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTREcut_S11_L002_I1_001.fastq.gz H27K5BCX2_KBTREcut_S11_L002_R1_001.fastq.gz H27K5BCX2_KBTREcut_S11_L002_R2_001.fastq.gz,fastq fastq fastq,918134580.0,6955565.0,GSM7676117 r5,0:8 1:26 2:98,A:198094257;C:139568875;G:152735838;T:191072590;N:173810,8,26,98,,198094257,139568875,152735838,191072590,173810,SRX21223191,SRS18479994,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91196,,0.11403,,0.85267,,0.50361,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24677,SRR25491978,SRX21223191,SRS18479994,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE cut replicate S11,GSM7676117,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE cut replicate S11,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676117,GSM7676117: KBTRE cut replicate S11; Danio rerio; RNA Seq,GSM7676117 r1,GSM7676117,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTREcut_S11_L002_I1_001.fastq.gz HFJ5GBCX2_KBTREcut_S11_L002_R1_001.fastq.gz HFJ5GBCX2_KBTREcut_S11_L002_R2_001.fastq.gz,fastq fastq fastq,868525152.0,6579736.0,GSM7676117 r6,0:8 1:26 2:98,A:187572958;C:132014722;G:144495273;T:180237409;N:493766,8,26,98,,187572958,132014722,144495273,180237409,493766,SRX21223191,SRS18479994,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91049,,0.11265,,0.85273,,0.49392,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24678,SRR25491979,SRX21223191,SRS18479994,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE cut replicate S11,GSM7676117,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE cut replicate S11,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676117,GSM7676117: KBTRE cut replicate S11; Danio rerio; RNA Seq,GSM7676117 r1,GSM7676117,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTREcut_S11_L002_I1_001.fastq.gz HYLGMBCXY_KBTREcut_S11_L002_R1_001.fastq.gz HYLGMBCXY_KBTREcut_S11_L002_R2_001.fastq.gz,fastq fastq fastq,967222872.0,7327446.0,GSM7676117 r7,0:8 1:26 2:98,A:208757589;C:146699883;G:160504752;T:198933585;N:3193899,8,26,98,,208757589,146699883,160504752,198933585,3193899,SRX21223191,SRS18479994,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91068,,0.11108,,0.85449,,0.48271,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24679,SRR25491980,SRX21223191,SRS18479994,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE cut replicate S11,GSM7676117,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE cut replicate S11,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676117,GSM7676117: KBTRE cut replicate S11; Danio rerio; RNA Seq,GSM7676117 r1,GSM7676117,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTREcut_S11_L002_I1_001.fastq.gz HYWGVBCXY_KBTREcut_S11_L002_R1_001.fastq.gz HYWGVBCXY_KBTREcut_S11_L002_R2_001.fastq.gz,fastq fastq fastq,918366636.0,6957323.0,GSM7676117 r8,0:8 1:26 2:98,A:198420992;C:139446089;G:152636322;T:191270874;N:43377,8,26,98,,198420992,139446089,152636322,191270874,43377,SRX21223191,SRS18479994,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91125,,0.11279,,0.85212,,0.49708,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24680,SRR25491981,SRX21223190,SRS18479993,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S8,GSM7676115,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S8,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676115,GSM7676115: KBTGR normal replicate S8; Danio rerio; RNA Seq,GSM7676115 r1,GSM7676115,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTGRnormal_S8_L001_I1_001.fastq.gz H27K5BCX2_KBTGRnormal_S8_L001_R1_001.fastq.gz H27K5BCX2_KBTGRnormal_S8_L001_R2_001.fastq.gz,fastq fastq fastq,1367764332.0,10361851.0,GSM7676115 r1,0:8 1:26 2:98,A:291792120;C:211871917;G:233940380;T:277543215;N:313766,8,26,98,,291792120,211871917,233940380,277543215,313766,SRX21223190,SRS18479993,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92841,,0.09159,,0.82191,,0.48306,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24681,SRR25491982,SRX21223190,SRS18479993,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S8,GSM7676115,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S8,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676115,GSM7676115: KBTGR normal replicate S8; Danio rerio; RNA Seq,GSM7676115 r1,GSM7676115,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTGRnormal_S8_L001_I1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S8_L001_R1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S8_L001_R2_001.fastq.gz,fastq fastq fastq,1324750284.0,10035987.0,GSM7676115 r2,0:8 1:26 2:98,A:282670428;C:205193043;G:226649784;T:268220709;N:792762,8,26,98,,282670428,205193043,226649784,268220709,792762,SRX21223190,SRS18479993,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92859,,0.09205,,0.82039,,0.48039,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24682,SRR25491983,SRX21223190,SRS18479993,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S8,GSM7676115,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S8,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676115,GSM7676115: KBTGR normal replicate S8; Danio rerio; RNA Seq,GSM7676115 r1,GSM7676115,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTGRnormal_S8_L001_I1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S8_L001_R1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S8_L001_R2_001.fastq.gz,fastq fastq fastq,1442154120.0,10925410.0,GSM7676115 r3,0:8 1:26 2:98,A:307172615;C:223150292;G:246311885;T:289234193;N:4821195,8,26,98,,307172615,223150292,246311885,289234193,4821195,SRX21223190,SRS18479993,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92841,,0.08941,,0.82331,,0.49215,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24683,SRR25491984,SRX21223190,SRS18479993,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S8,GSM7676115,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S8,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676115,GSM7676115: KBTGR normal replicate S8; Danio rerio; RNA Seq,GSM7676115 r1,GSM7676115,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTGRnormal_S8_L001_I1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S8_L001_R1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S8_L001_R2_001.fastq.gz,fastq fastq fastq,1358634684.0,10292687.0,GSM7676115 r4,0:8 1:26 2:98,A:290016958;C:210290529;G:232317191;T:275847772;N:210876,8,26,98,,290016958,210290529,232317191,275847772,210876,SRX21223190,SRS18479993,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92745,,0.09192,,0.82229,,0.49666,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24684,SRR25491985,SRX21223190,SRS18479993,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S8,GSM7676115,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S8,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676115,GSM7676115: KBTGR normal replicate S8; Danio rerio; RNA Seq,GSM7676115 r1,GSM7676115,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTGRnormal_S8_L002_I1_001.fastq.gz H27K5BCX2_KBTGRnormal_S8_L002_R1_001.fastq.gz H27K5BCX2_KBTGRnormal_S8_L002_R2_001.fastq.gz,fastq fastq fastq,1353664092.0,10255031.0,GSM7676115 r5,0:8 1:26 2:98,A:288847376;C:209739068;G:231593033;T:274552362;N:261199,8,26,98,,288847376,209739068,231593033,274552362,261199,SRX21223190,SRS18479993,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92838,,0.09211,,0.82207,,0.48301,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24685,SRR25491986,SRX21223190,SRS18479993,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S8,GSM7676115,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S8,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676115,GSM7676115: KBTGR normal replicate S8; Danio rerio; RNA Seq,GSM7676115 r1,GSM7676115,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTGRnormal_S8_L002_I1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S8_L002_R1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S8_L002_R2_001.fastq.gz,fastq fastq fastq,1282964496.0,9719428.0,GSM7676115 r6,0:8 1:26 2:98,A:273803342;C:198769671;G:219587842;T:259615174;N:727915,8,26,98,,273803342,198769671,219587842,259615174,727915,SRX21223190,SRS18479993,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92815,,0.09094,,0.82189,,0.47933,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24686,SRR25491987,SRX21223190,SRS18479993,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S8,GSM7676115,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S8,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676115,GSM7676115: KBTGR normal replicate S8; Danio rerio; RNA Seq,GSM7676115 r1,GSM7676115,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTGRnormal_S8_L002_I1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S8_L002_R1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S8_L002_R2_001.fastq.gz,fastq fastq fastq,1425314880.0,10797840.0,GSM7676115 r7,0:8 1:26 2:98,A:303654013;C:220453444;G:243409971;T:285937241;N:4733651,8,26,98,,303654013,220453444,243409971,285937241,4733651,SRX21223190,SRS18479993,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92724,,0.09059,,0.82345,,0.49626,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24687,SRR25491988,SRX21223190,SRS18479993,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S8,GSM7676115,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S8,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676115,GSM7676115: KBTGR normal replicate S8; Danio rerio; RNA Seq,GSM7676115 r1,GSM7676115,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTGRnormal_S8_L002_I1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S8_L002_R1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S8_L002_R2_001.fastq.gz,fastq fastq fastq,1358584788.0,10292309.0,GSM7676115 r8,0:8 1:26 2:98,A:290131069;C:210271668;G:232237599;T:275940105;N:65841,8,26,98,,290131069,210271668,232237599,275940105,65841,SRX21223190,SRS18479993,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92858,,0.09144,,0.82089,,0.49057,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24688,SRR25491991,SRX21223189,SRS18479992,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S7,GSM7676114,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S7,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676114,GSM7676114: KBTGR normal replicate S7; Danio rerio; RNA Seq,GSM7676114 r1,GSM7676114,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTGRnormal_S7_L001_I1_001.fastq.gz H27K5BCX2_KBTGRnormal_S7_L001_R1_001.fastq.gz H27K5BCX2_KBTGRnormal_S7_L001_R2_001.fastq.gz,fastq fastq fastq,1045774224.0,7922532.0,GSM7676114 r1,0:8 1:26 2:98,A:224743708;C:161896286;G:178467180;T:211061243;N:239719,8,26,98,,224743708,161896286,178467180,211061243,239719,SRX21223189,SRS18479992,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92898,,0.0948,,0.82576,,0.48767,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24689,SRR25491992,SRX21223189,SRS18479992,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S7,GSM7676114,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S7,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676114,GSM7676114: KBTGR normal replicate S7; Danio rerio; RNA Seq,GSM7676114 r1,GSM7676114,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTGRnormal_S7_L001_I1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S7_L001_R1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S7_L001_R2_001.fastq.gz,fastq fastq fastq,1023737880.0,7755590.0,GSM7676114 r2,0:8 1:26 2:98,A:220339751;C:158506697;G:174717320;T:205879340;N:604712,8,26,98,,220339751,158506697,174717320,205879340,604712,SRX21223189,SRS18479992,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.93138,,0.09445,,0.82319,,0.49095,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24690,SRR25491993,SRX21223189,SRS18479992,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S7,GSM7676114,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S7,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676114,GSM7676114: KBTGR normal replicate S7; Danio rerio; RNA Seq,GSM7676114 r1,GSM7676114,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTGRnormal_S7_L001_I1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S7_L001_R1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S7_L001_R2_001.fastq.gz,fastq fastq fastq,1107722484.0,8391837.0,GSM7676114 r3,0:8 1:26 2:98,A:237628383;C:171310823;G:188847113;T:220892571;N:3721136,8,26,98,,237628383,171310823,188847113,220892571,3721136,SRX21223189,SRS18479992,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92932,,0.09165,,0.82432,,0.48843,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24691,SRR25491994,SRX21223189,SRS18479992,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S7,GSM7676114,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S7,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676114,GSM7676114: KBTGR normal replicate S7; Danio rerio; RNA Seq,GSM7676114 r1,GSM7676114,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTGRnormal_S7_L001_I1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S7_L001_R1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S7_L001_R2_001.fastq.gz,fastq fastq fastq,1018155600.0,7713300.0,GSM7676114 r4,0:8 1:26 2:98,A:218785960;C:157467573;G:173782025;T:205710180;N:157662,8,26,98,,218785960,157467573,173782025,205710180,157662,SRX21223189,SRS18479992,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92735,,0.09294,,0.82304,,0.48936,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24692,SRR25491995,SRX21223189,SRS18479992,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S7,GSM7676114,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S7,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676114,GSM7676114: KBTGR normal replicate S7; Danio rerio; RNA Seq,GSM7676114 r1,GSM7676114,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTGRnormal_S7_L002_I1_001.fastq.gz H27K5BCX2_KBTGRnormal_S7_L002_R1_001.fastq.gz H27K5BCX2_KBTGRnormal_S7_L002_R2_001.fastq.gz,fastq fastq fastq,1037896992.0,7862856.0,GSM7676114 r5,0:8 1:26 2:98,A:222624793;C:160770752;G:177337819;T:209629234;N:197290,8,26,98,,222624793,160770752,177337819,209629234,197290,SRX21223189,SRS18479992,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.93038,,0.09291,,0.82513,,0.48834,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24693,SRR25491996,SRX21223189,SRS18479992,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S7,GSM7676114,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S7,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676114,GSM7676114: KBTGR normal replicate S7; Danio rerio; RNA Seq,GSM7676114 r1,GSM7676114,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTGRnormal_S7_L002_I1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S7_L002_R1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S7_L002_R2_001.fastq.gz,fastq fastq fastq,994648116.0,7535213.0,GSM7676114 r6,0:8 1:26 2:98,A:213918528;C:154046950;G:169913173;T:200006956;N:565267,8,26,98,,213918528,154046950,169913173,200006956,565267,SRX21223189,SRS18479992,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92863,,0.09237,,0.8244,,0.48574,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24694,SRR25491997,SRX21223189,SRS18479992,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S7,GSM7676114,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S7,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676114,GSM7676114: KBTGR normal replicate S7; Danio rerio; RNA Seq,GSM7676114 r1,GSM7676114,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTGRnormal_S7_L002_I1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S7_L002_R1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S7_L002_R2_001.fastq.gz,fastq fastq fastq,1095910068.0,8302349.0,GSM7676114 r7,0:8 1:26 2:98,A:235361030;C:169424678;G:186752468;T:218466797;N:3625229,8,26,98,,235361030,169424678,186752468,218466797,3625229,SRX21223189,SRS18479992,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92887,,0.09019,,0.82696,,0.4934,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24695,SRR25491998,SRX21223189,SRS18479992,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S7,GSM7676114,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S7,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676114,GSM7676114: KBTGR normal replicate S7; Danio rerio; RNA Seq,GSM7676114 r1,GSM7676114,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTGRnormal_S7_L002_I1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S7_L002_R1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S7_L002_R2_001.fastq.gz,fastq fastq fastq,1020164640.0,7728520.0,GSM7676114 r8,0:8 1:26 2:98,A:219455597;C:157669416;G:174033845;T:206187545;N:48557,8,26,98,,219455597,157669416,174033845,206187545,48557,SRX21223189,SRS18479992,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.93,,0.0929,,0.82507,,0.48822,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24696,SRR25491999,SRX21223188,SRS18479991,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S6,GSM7676113,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S6,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676113,GSM7676113: KBTGR normal replicate S6; Danio rerio; RNA Seq,GSM7676113 r1,GSM7676113,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTGRnormal_S6_L001_I1_001.fastq.gz H27K5BCX2_KBTGRnormal_S6_L001_R1_001.fastq.gz H27K5BCX2_KBTGRnormal_S6_L001_R2_001.fastq.gz,fastq fastq fastq,1289409660.0,9768255.0,GSM7676113 r1,0:8 1:26 2:98,A:275297633;C:199461255;G:220403674;T:261830960;N:295468,8,26,98,,275297633,199461255,220403674,261830960,295468,SRX21223188,SRS18479991,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92761,,0.09178,,0.82089,,0.49952,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24697,SRR25492000,SRX21223188,SRS18479991,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S6,GSM7676113,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S6,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676113,GSM7676113: KBTGR normal replicate S6; Danio rerio; RNA Seq,GSM7676113 r1,GSM7676113,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTGRnormal_S6_L001_I1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S6_L001_R1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S6_L001_R2_001.fastq.gz,fastq fastq fastq,1254104148.0,9500789.0,GSM7676113 r2,0:8 1:26 2:98,A:267759276;C:194047461;G:214469796;T:254057804;N:742985,8,26,98,,267759276,194047461,214469796,254057804,742985,SRX21223188,SRS18479991,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92863,,0.09263,,0.82016,,0.49849,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24698,SRR25492001,SRX21223188,SRS18479991,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S6,GSM7676113,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S6,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676113,GSM7676113: KBTGR normal replicate S6; Danio rerio; RNA Seq,GSM7676113 r1,GSM7676113,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTGRnormal_S6_L001_I1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S6_L001_R1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S6_L001_R2_001.fastq.gz,fastq fastq fastq,1364037444.0,10333617.0,GSM7676113 r3,0:8 1:26 2:98,A:290782963;C:210764004;G:232828321;T:273741440;N:4577738,8,26,98,,290782963,210764004,232828321,273741440,4577738,SRX21223188,SRS18479991,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92727,,0.09037,,0.82339,,0.49743,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24699,SRR25492002,SRX21223188,SRS18479991,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S6,GSM7676113,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S6,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676113,GSM7676113: KBTGR normal replicate S6; Danio rerio; RNA Seq,GSM7676113 r1,GSM7676113,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTGRnormal_S6_L001_I1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S6_L001_R1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S6_L001_R2_001.fastq.gz,fastq fastq fastq,1274535900.0,9655575.0,GSM7676113 r4,0:8 1:26 2:98,A:272331035;C:196919570;G:217674747;T:259126322;N:194676,8,26,98,,272331035,196919570,217674747,259126322,194676,SRX21223188,SRS18479991,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.9267,,0.09131,,0.82193,,0.49736,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24700,SRR25492003,SRX21223188,SRS18479991,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S6,GSM7676113,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S6,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676113,GSM7676113: KBTGR normal replicate S6; Danio rerio; RNA Seq,GSM7676113 r1,GSM7676113,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTGRnormal_S6_L002_I1_001.fastq.gz H27K5BCX2_KBTGRnormal_S6_L002_R1_001.fastq.gz H27K5BCX2_KBTGRnormal_S6_L002_R2_001.fastq.gz,fastq fastq fastq,1278788544.0,9687792.0,GSM7676113 r5,0:8 1:26 2:98,A:273089526;C:197794682;G:218629305;T:259640660;N:249443,8,26,98,,273089526,197794682,218629305,259640660,249443,SRX21223188,SRS18479991,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92837,,0.09211,,0.82069,,0.49043,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24701,SRR25492004,SRX21223188,SRS18479991,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S6,GSM7676113,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S6,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676113,GSM7676113: KBTGR normal replicate S6; Danio rerio; RNA Seq,GSM7676113 r1,GSM7676113,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTGRnormal_S6_L002_I1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S6_L002_R1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S6_L002_R2_001.fastq.gz,fastq fastq fastq,1218538200.0,9231350.0,GSM7676113 r6,0:8 1:26 2:98,A:260174350;C:188588952;G:208442781;T:246771528;N:694689,8,26,98,,260174350,188588952,208442781,246771528,694689,SRX21223188,SRS18479991,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92755,,0.09174,,0.82152,,0.48524,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24702,SRR25492005,SRX21223188,SRS18479991,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S6,GSM7676113,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S6,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676113,GSM7676113: KBTGR normal replicate S6; Danio rerio; RNA Seq,GSM7676113 r1,GSM7676113,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTGRnormal_S6_L002_I1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S6_L002_R1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S6_L002_R2_001.fastq.gz,fastq fastq fastq,1348885428.0,10218829.0,GSM7676113 r7,0:8 1:26 2:98,A:287599265;C:208361077;G:230218011;T:270815023;N:4451866,8,26,98,,287599265,208361077,230218011,270815023,4451866,SRX21223188,SRS18479991,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92616,,0.08938,,0.82189,,0.49517,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24703,SRR25492006,SRX21223188,SRS18479991,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S6,GSM7676113,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S6,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676113,GSM7676113: KBTGR normal replicate S6; Danio rerio; RNA Seq,GSM7676113 r1,GSM7676113,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTGRnormal_S6_L002_I1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S6_L002_R1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S6_L002_R2_001.fastq.gz,fastq fastq fastq,1274044596.0,9651853.0,GSM7676113 r8,0:8 1:26 2:98,A:272274110;C:196868273;G:217614843;T:259062639;N:61729,8,26,98,,272274110,196868273,217614843,259062639,61729,SRX21223188,SRS18479991,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92673,,0.09105,,0.82142,,0.48867,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24704,SRR25492007,SRX21223187,SRS18479990,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S5,GSM7676112,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S5,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676112,GSM7676112: KBTGR normal replicate S5; Danio rerio; RNA Seq,GSM7676112 r1,GSM7676112,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTGRnormal_S5_L001_I1_001.fastq.gz H27K5BCX2_KBTGRnormal_S5_L001_R1_001.fastq.gz H27K5BCX2_KBTGRnormal_S5_L001_R2_001.fastq.gz,fastq fastq fastq,1258754244.0,9536017.0,GSM7676112 r1,0:8 1:26 2:98,A:269418553;C:194370105;G:214652075;T:255806804;N:282129,8,26,98,,269418553,194370105,214652075,255806804,282129,SRX21223187,SRS18479990,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.9286,,0.09296,,0.82288,,0.48038,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24705,SRR25492008,SRX21223187,SRS18479990,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S5,GSM7676112,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S5,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676112,GSM7676112: KBTGR normal replicate S5; Danio rerio; RNA Seq,GSM7676112 r1,GSM7676112,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTGRnormal_S5_L001_I1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S5_L001_R1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S5_L001_R2_001.fastq.gz,fastq fastq fastq,1217159724.0,9220907.0,GSM7676112 r2,0:8 1:26 2:98,A:260789467;C:187945962;G:207550436;T:246642449;N:720572,8,26,98,,260789467,187945962,207550436,246642449,720572,SRX21223187,SRS18479990,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.93045,,0.09356,,0.82386,,0.4736,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24706,SRR25492009,SRX21223187,SRS18479990,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S5,GSM7676112,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S5,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676112,GSM7676112: KBTGR normal replicate S5; Danio rerio; RNA Seq,GSM7676112 r1,GSM7676112,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTGRnormal_S5_L001_I1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S5_L001_R1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S5_L001_R2_001.fastq.gz,fastq fastq fastq,1327996824.0,10060582.0,GSM7676112 r3,0:8 1:26 2:98,A:283722392;C:204894097;G:226054109;T:266823827;N:4442611,8,26,98,,283722392,204894097,226054109,266823827,4442611,SRX21223187,SRS18479990,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92793,,0.09118,,0.82513,,0.48007,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24707,SRR25492010,SRX21223187,SRS18479990,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S5,GSM7676112,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S5,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676112,GSM7676112: KBTGR normal replicate S5; Danio rerio; RNA Seq,GSM7676112 r1,GSM7676112,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTGRnormal_S5_L001_I1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S5_L001_R1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S5_L001_R2_001.fastq.gz,fastq fastq fastq,1255655808.0,9512544.0,GSM7676112 r4,0:8 1:26 2:98,A:268848025;C:193752306;G:214061624;T:255371933;N:195424,8,26,98,,268848025,193752306,214061624,255371933,195424,SRX21223187,SRS18479990,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92719,,0.09327,,0.82221,,0.47626,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24708,SRR25492011,SRX21223187,SRS18479990,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S5,GSM7676112,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S5,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676112,GSM7676112: KBTGR normal replicate S5; Danio rerio; RNA Seq,GSM7676112 r1,GSM7676112,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTGRnormal_S5_L002_I1_001.fastq.gz H27K5BCX2_KBTGRnormal_S5_L002_R1_001.fastq.gz H27K5BCX2_KBTGRnormal_S5_L002_R2_001.fastq.gz,fastq fastq fastq,1246449072.0,9442796.0,GSM7676112 r5,0:8 1:26 2:98,A:266772235;C:192514744;G:212592908;T:253285733;N:228388,8,26,98,,266772235,192514744,212592908,253285733,228388,SRX21223187,SRS18479990,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92776,,0.09295,,0.82333,,0.48441,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24709,SRR25492012,SRX21223187,SRS18479990,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S5,GSM7676112,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S5,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676112,GSM7676112: KBTGR normal replicate S5; Danio rerio; RNA Seq,GSM7676112 r1,GSM7676112,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTGRnormal_S5_L002_I1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S5_L002_R1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S5_L002_R2_001.fastq.gz,fastq fastq fastq,1176943812.0,8916241.0,GSM7676112 r6,0:8 1:26 2:98,A:252114687;C:181782204;G:200782194;T:238444957;N:667576,8,26,98,,252114687,181782204,200782194,238444957,667576,SRX21223187,SRS18479990,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92798,,0.09407,,0.82225,,0.47898,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24710,SRR25492013,SRX21223187,SRS18479990,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S5,GSM7676112,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S5,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676112,GSM7676112: KBTGR normal replicate S5; Danio rerio; RNA Seq,GSM7676112 r1,GSM7676112,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTGRnormal_S5_L002_I1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S5_L002_R1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S5_L002_R2_001.fastq.gz,fastq fastq fastq,1312162368.0,9940624.0,GSM7676112 r7,0:8 1:26 2:98,A:280415120;C:202362829;G:223408996;T:263680714;N:4313493,8,26,98,,280415120,202362829,223408996,263680714,4313493,SRX21223187,SRS18479990,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.9269,,0.09153,,0.82386,,0.48775,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24711,SRR25492014,SRX21223187,SRS18479990,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR normal replicate S5,GSM7676112,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR normal replicate S5,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676112,GSM7676112: KBTGR normal replicate S5; Danio rerio; RNA Seq,GSM7676112 r1,GSM7676112,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTGRnormal_S5_L002_I1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S5_L002_R1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S5_L002_R2_001.fastq.gz,fastq fastq fastq,1254798732.0,9506051.0,GSM7676112 r8,0:8 1:26 2:98,A:268758608;C:193670297;G:213835768;T:255268464;N:59861,8,26,98,,268758608,193670297,213835768,255268464,59861,SRX21223187,SRS18479990,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.9283,,0.09341,,0.82211,,0.49121,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24712,SRR25492015,SRX21223186,SRS18479989,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR cut replicate S16,GSM7676111,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR cut replicate S16,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676111,GSM7676111: KBTGR cut replicate S16; Danio rerio; RNA Seq,GSM7676111 r1,GSM7676111,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTGRcut_S16_L001_I1_001.fastq.gz H27K5BCX2_KBTGRcut_S16_L001_R1_001.fastq.gz H27K5BCX2_KBTGRcut_S16_L001_R2_001.fastq.gz,fastq fastq fastq,1733777364.0,13134677.0,GSM7676111 r1,0:8 1:26 2:98,A:377310857;C:268033707;G:292815269;T:348639631;N:398882,8,26,98,,377310857,268033707,292815269,348639631,398882,SRX21223186,SRS18479989,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92457,,0.10972,,0.83684,,0.49054,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24713,SRR25492016,SRX21223186,SRS18479989,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR cut replicate S16,GSM7676111,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR cut replicate S16,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676111,GSM7676111: KBTGR cut replicate S16; Danio rerio; RNA Seq,GSM7676111 r1,GSM7676111,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTGRcut_S16_L001_I1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S16_L001_R1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S16_L001_R2_001.fastq.gz,fastq fastq fastq,1693931844.0,12832817.0,GSM7676111 r2,0:8 1:26 2:98,A:370335488;C:261641086;G:285793090;T:338853348;N:993054,8,26,98,,370335488,261641086,285793090,338853348,993054,SRX21223186,SRS18479989,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.9257,,0.11044,,0.83593,,0.49929,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24714,SRR25492017,SRX21223186,SRS18479989,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR cut replicate S16,GSM7676111,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR cut replicate S16,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676111,GSM7676111: KBTGR cut replicate S16; Danio rerio; RNA Seq,GSM7676111 r1,GSM7676111,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTGRcut_S16_L001_I1_001.fastq.gz HYLGMBCXY_KBTGRcut_S16_L001_R1_001.fastq.gz HYLGMBCXY_KBTGRcut_S16_L001_R2_001.fastq.gz,fastq fastq fastq,1822627488.0,13807784.0,GSM7676111 r3,0:8 1:26 2:98,A:396109320;C:281479505;G:307344748;T:362166256;N:6063003,8,26,98,,396109320,281479505,307344748,362166256,6063003,SRX21223186,SRS18479989,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.9237,,0.1075,,0.83733,,0.49995,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24715,SRR25492018,SRX21223186,SRS18479989,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR cut replicate S16,GSM7676111,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR cut replicate S16,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676111,GSM7676111: KBTGR cut replicate S16; Danio rerio; RNA Seq,GSM7676111 r1,GSM7676111,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTGRcut_S16_L001_I1_001.fastq.gz HYWGVBCXY_KBTGRcut_S16_L001_R1_001.fastq.gz HYWGVBCXY_KBTGRcut_S16_L001_R2_001.fastq.gz,fastq fastq fastq,1686941784.0,12779862.0,GSM7676111 r4,0:8 1:26 2:98,A:366995826;C:260455612;G:284984185;T:339737397;N:253456,8,26,98,,366995826,260455612,284984185,339737397,253456,SRX21223186,SRS18479989,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92245,,0.10934,,0.83583,,0.5109,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24716,SRR25492019,SRX21223186,SRS18479989,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR cut replicate S16,GSM7676111,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR cut replicate S16,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676111,GSM7676111: KBTGR cut replicate S16; Danio rerio; RNA Seq,GSM7676111 r1,GSM7676111,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTGRcut_S16_L002_I1_001.fastq.gz HYLGMBCXY_KBTGRcut_S16_L002_R1_001.fastq.gz HYLGMBCXY_KBTGRcut_S16_L002_R2_001.fastq.gz,fastq fastq fastq,1800605268.0,13640949.0,GSM7676111 r7,0:8 1:26 2:98,A:392033512;C:277884536;G:303332072;T:357657308;N:5905574,8,26,98,,392033512,277884536,303332072,357657308,5905574,SRX21223186,SRS18479989,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92264,,0.10865,,0.83771,,0.4962,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24717,SRR25492020,SRX21223186,SRS18479989,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR cut replicate S16,GSM7676111,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR cut replicate S16,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676111,GSM7676111: KBTGR cut replicate S16; Danio rerio; RNA Seq,GSM7676111 r1,GSM7676111,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTGRcut_S16_L002_I1_001.fastq.gz HYWGVBCXY_KBTGRcut_S16_L002_R1_001.fastq.gz HYWGVBCXY_KBTGRcut_S16_L002_R2_001.fastq.gz,fastq fastq fastq,1687212120.0,12781910.0,GSM7676111 r8,0:8 1:26 2:98,A:367591713;C:260374660;G:284790982;T:339790038;N:79787,8,26,98,,367591713,260374660,284790982,339790038,79787,SRX21223186,SRS18479989,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92439,,0.11008,,0.83252,,0.48566,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24718,SRR25492035,SRX21223186,SRS18479989,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR cut replicate S16,GSM7676111,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR cut replicate S16,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676111,GSM7676111: KBTGR cut replicate S16; Danio rerio; RNA Seq,GSM7676111 r1,GSM7676111,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTGRcut_S16_L002_I1_001.fastq.gz H27K5BCX2_KBTGRcut_S16_L002_R1_001.fastq.gz H27K5BCX2_KBTGRcut_S16_L002_R2_001.fastq.gz,fastq fastq fastq,1715599116.0,12996963.0,GSM7676111 r5,0:8 1:26 2:98,A:372113041;C:265506989;G:290255809;T:345508071;N:318464,8,26,98,,372113041,265506989,290255809,345508071,318464,SRX21223186,SRS18479989,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92368,,0.10681,,0.83727,,0.49306,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24719,SRR25492036,SRX21223186,SRS18479989,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR cut replicate S16,GSM7676111,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR cut replicate S16,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676111,GSM7676111: KBTGR cut replicate S16; Danio rerio; RNA Seq,GSM7676111 r1,GSM7676111,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTGRcut_S16_L002_I1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S16_L002_R1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S16_L002_R2_001.fastq.gz,fastq fastq fastq,1643667564.0,12452027.0,GSM7676111 r6,0:8 1:26 2:98,A:358646057;C:254091415;G:277620310;T:329013074;N:927790,8,26,98,,358646057,254091415,277620310,329013074,927790,SRX21223186,SRS18479989,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92527,,0.1079,,0.83465,,0.49184,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24720,SRR25492021,SRX21223185,SRS18479988,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE normal replicate S2,GSM7676121,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE normal replicate S2,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676121,GSM7676121: KBTRE normal replicate S2; Danio rerio; RNA Seq,GSM7676121 r1,GSM7676121,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTREnormal_S2_L001_I1_001.fastq.gz H27K5BCX2_KBTREnormal_S2_L001_R1_001.fastq.gz H27K5BCX2_KBTREnormal_S2_L001_R2_001.fastq.gz,fastq fastq fastq,807188844.0,6115067.0,GSM7676121 r1,0:8 1:26 2:98,A:172308620;C:125913345;G:139442237;T:161426336;N:186028,8,26,98,,172308620,125913345,139442237,161426336,186028,SRX21223185,SRS18479988,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92298,,0.08811,,0.85433,,0.4736,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24721,SRR25492022,SRX21223185,SRS18479988,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE normal replicate S2,GSM7676121,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE normal replicate S2,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676121,GSM7676121: KBTRE normal replicate S2; Danio rerio; RNA Seq,GSM7676121 r1,GSM7676121,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTREnormal_S2_L001_I1_001.fastq.gz HFJ5GBCX2_KBTREnormal_S2_L001_R1_001.fastq.gz HFJ5GBCX2_KBTREnormal_S2_L001_R2_001.fastq.gz,fastq fastq fastq,793147344.0,6008692.0,GSM7676121 r2,0:8 1:26 2:98,A:169497439;C:123759266;G:137078289;T:158052236;N:464586,8,26,98,,169497439,123759266,137078289,158052236,464586,SRX21223185,SRS18479988,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92361,,0.08644,,0.85464,,0.47495,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24722,SRR25492023,SRX21223185,SRS18479988,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE normal replicate S2,GSM7676121,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE normal replicate S2,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676121,GSM7676121: KBTRE normal replicate S2; Danio rerio; RNA Seq,GSM7676121 r1,GSM7676121,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTREnormal_S2_L001_I1_001.fastq.gz HYLGMBCXY_KBTREnormal_S2_L001_R1_001.fastq.gz HYLGMBCXY_KBTREnormal_S2_L001_R2_001.fastq.gz,fastq fastq fastq,852294828.0,6456779.0,GSM7676121 r3,0:8 1:26 2:98,A:181361509;C:132917413;G:147157966;T:168488477;N:2838977,8,26,98,,181361509,132917413,147157966,168488477,2838977,SRX21223185,SRS18479988,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.9234,,0.08441,,0.85681,,0.45235,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24723,SRR25492024,SRX21223185,SRS18479988,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE normal replicate S2,GSM7676121,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE normal replicate S2,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676121,GSM7676121: KBTRE normal replicate S2; Danio rerio; RNA Seq,GSM7676121 r1,GSM7676121,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTREnormal_S2_L001_I1_001.fastq.gz HYWGVBCXY_KBTREnormal_S2_L001_R1_001.fastq.gz HYWGVBCXY_KBTREnormal_S2_L001_R2_001.fastq.gz,fastq fastq fastq,781758516.0,5922413.0,GSM7676121 r4,0:8 1:26 2:98,A:166724753;C:121839518;G:135085811;T:156626231;N:120161,8,26,98,,166724753,121839518,135085811,156626231,120161,SRX21223185,SRS18479988,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92293,,0.08698,,0.85626,,0.47803,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24724,SRR25492025,SRX21223185,SRS18479988,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE normal replicate S2,GSM7676121,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE normal replicate S2,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676121,GSM7676121: KBTRE normal replicate S2; Danio rerio; RNA Seq,GSM7676121 r1,GSM7676121,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTREnormal_S2_L002_I1_001.fastq.gz HYLGMBCXY_KBTREnormal_S2_L002_R1_001.fastq.gz HYLGMBCXY_KBTREnormal_S2_L002_R2_001.fastq.gz,fastq fastq fastq,843137856.0,6387408.0,GSM7676121 r7,0:8 1:26 2:98,A:179558862;C:131385546;G:145540868;T:166696387;N:2784321,8,26,98,,179558862,131385546,145540868,166696387,2784321,SRX21223185,SRS18479988,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92281,,0.08446,,0.85685,,0.47524,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24725,SRR25492026,SRX21223185,SRS18479988,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE normal replicate S2,GSM7676121,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE normal replicate S2,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676121,GSM7676121: KBTRE normal replicate S2; Danio rerio; RNA Seq,GSM7676121 r1,GSM7676121,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTREnormal_S2_L002_I1_001.fastq.gz HYWGVBCXY_KBTREnormal_S2_L002_R1_001.fastq.gz HYWGVBCXY_KBTREnormal_S2_L002_R2_001.fastq.gz,fastq fastq fastq,782789964.0,5930227.0,GSM7676121 r8,0:8 1:26 2:98,A:167092677;C:121959994;G:135189997;T:156882004;N:37574,8,26,98,,167092677,121959994,135189997,156882004,37574,SRX21223185,SRS18479988,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92384,,0.08593,,0.85529,,0.47658,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24726,SRR25492073,SRX21223185,SRS18479988,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE normal replicate S2,GSM7676121,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE normal replicate S2,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676121,GSM7676121: KBTRE normal replicate S2; Danio rerio; RNA Seq,GSM7676121 r1,GSM7676121,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTREnormal_S2_L002_I1_001.fastq.gz H27K5BCX2_KBTREnormal_S2_L002_R1_001.fastq.gz H27K5BCX2_KBTREnormal_S2_L002_R2_001.fastq.gz,fastq fastq fastq,799492452.0,6056761.0,GSM7676121 r5,0:8 1:26 2:98,A:170481537;C:124727025;G:138222223;T:159980825;N:150968,8,26,98,,170481537,124727025,138222223,159980825,150968,SRX21223185,SRS18479988,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92219,,0.08693,,0.85689,,0.45239,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24727,SRR25492074,SRX21223185,SRS18479988,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE normal replicate S2,GSM7676121,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE normal replicate S2,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676121,GSM7676121: KBTRE normal replicate S2; Danio rerio; RNA Seq,GSM7676121 r1,GSM7676121,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTREnormal_S2_L002_I1_001.fastq.gz HFJ5GBCX2_KBTREnormal_S2_L002_R1_001.fastq.gz HFJ5GBCX2_KBTREnormal_S2_L002_R2_001.fastq.gz,fastq fastq fastq,771619332.0,5845601.0,GSM7676121 r6,0:8 1:26 2:98,A:164827141;C:120458327;G:133444180;T:153706468;N:432782,8,26,98,,164827141,120458327,133444180,153706468,432782,SRX21223185,SRS18479988,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.9244,,0.086,,0.85752,,0.46487,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24728,SRR25492027,SRX21223184,SRS18479986,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR cut replicate S15,GSM7676110,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR cut replicate S15,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676110,GSM7676110: KBTGR cut replicate S15; Danio rerio; RNA Seq,GSM7676110 r1,GSM7676110,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTGRcut_S15_L001_I1_001.fastq.gz H27K5BCX2_KBTGRcut_S15_L001_R1_001.fastq.gz H27K5BCX2_KBTGRcut_S15_L001_R2_001.fastq.gz,fastq fastq fastq,991634028.0,7512379.0,GSM7676110 r1,0:8 1:26 2:98,A:213910719;C:153374311;G:167803904;T:200905324;N:218884,8,26,98,,213910719,153374311,167803904,200905324,218884,SRX21223184,SRS18479986,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92289,,0.10915,,0.83163,,0.51061,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24729,SRR25492028,SRX21223184,SRS18479986,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR cut replicate S15,GSM7676110,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR cut replicate S15,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676110,GSM7676110: KBTGR cut replicate S15; Danio rerio; RNA Seq,GSM7676110 r1,GSM7676110,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTGRcut_S15_L001_I1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S15_L001_R1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S15_L001_R2_001.fastq.gz,fastq fastq fastq,973359420.0,7373935.0,GSM7676110 r2,0:8 1:26 2:98,A:210076453;C:150636615;G:164768683;T:196577221;N:586658,8,26,98,,210076453,150636615,164768683,196577221,586658,SRX21223184,SRS18479986,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92307,,0.10829,,0.8309,,0.50664,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24730,SRR25492029,SRX21223184,SRS18479986,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR cut replicate S15,GSM7676110,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR cut replicate S15,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676110,GSM7676110: KBTGR cut replicate S15; Danio rerio; RNA Seq,GSM7676110 r1,GSM7676110,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTGRcut_S15_L001_I1_001.fastq.gz HYLGMBCXY_KBTGRcut_S15_L001_R1_001.fastq.gz HYLGMBCXY_KBTGRcut_S15_L001_R2_001.fastq.gz,fastq fastq fastq,1041506532.0,7890201.0,GSM7676110 r3,0:8 1:26 2:98,A:224331472;C:160956885;G:176036393;T:208465176;N:3449772,8,26,98,,224331472,160956885,176036393,208465176,3449772,SRX21223184,SRS18479986,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92046,,0.10509,,0.83179,,0.5158,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24731,SRR25492030,SRX21223184,SRS18479986,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR cut replicate S15,GSM7676110,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR cut replicate S15,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676110,GSM7676110: KBTGR cut replicate S15; Danio rerio; RNA Seq,GSM7676110 r1,GSM7676110,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTGRcut_S15_L001_I1_001.fastq.gz HYWGVBCXY_KBTGRcut_S15_L001_R1_001.fastq.gz HYWGVBCXY_KBTGRcut_S15_L001_R2_001.fastq.gz,fastq fastq fastq,959532816.0,7269188.0,GSM7676110 r4,0:8 1:26 2:98,A:207101192;C:148189510;G:162346748;T:194597135;N:145839,8,26,98,,207101192,148189510,162346748,194597135,145839,SRX21223184,SRS18479986,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92159,,0.10724,,0.83031,,0.51032,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24732,SRR25492031,SRX21223184,SRS18479986,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR cut replicate S15,GSM7676110,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR cut replicate S15,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676110,GSM7676110: KBTGR cut replicate S15; Danio rerio; RNA Seq,GSM7676110 r1,GSM7676110,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTGRcut_S15_L002_I1_001.fastq.gz H27K5BCX2_KBTGRcut_S15_L002_R1_001.fastq.gz H27K5BCX2_KBTGRcut_S15_L002_R2_001.fastq.gz,fastq fastq fastq,981662748.0,7436839.0,GSM7676110 r5,0:8 1:26 2:98,A:211518289;C:151920644;G:166249815;T:198931555;N:189919,8,26,98,,211518289,151920644,166249815,198931555,189919,SRX21223184,SRS18479986,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92149,,0.10822,,0.83078,,0.51544,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24733,SRR25492032,SRX21223184,SRS18479986,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR cut replicate S15,GSM7676110,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR cut replicate S15,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676110,GSM7676110: KBTGR cut replicate S15; Danio rerio; RNA Seq,GSM7676110 r1,GSM7676110,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTGRcut_S15_L002_I1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S15_L002_R1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S15_L002_R2_001.fastq.gz,fastq fastq fastq,945758088.0,7164834.0,GSM7676110 r6,0:8 1:26 2:98,A:203967307;C:146422295;G:160254376;T:190978208;N:531546,8,26,98,,203967307,146422295,160254376,190978208,531546,SRX21223184,SRS18479986,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92245,,0.10759,,0.83142,,0.51632,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24734,SRR25492033,SRX21223184,SRS18479986,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR cut replicate S15,GSM7676110,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR cut replicate S15,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676110,GSM7676110: KBTGR cut replicate S15; Danio rerio; RNA Seq,GSM7676110 r1,GSM7676110,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTGRcut_S15_L002_I1_001.fastq.gz HYLGMBCXY_KBTGRcut_S15_L002_R1_001.fastq.gz HYLGMBCXY_KBTGRcut_S15_L002_R2_001.fastq.gz,fastq fastq fastq,1029633660.0,7800255.0,GSM7676110 r7,0:8 1:26 2:98,A:221920698;C:159045837;G:173908417;T:206140930;N:3409108,8,26,98,,221920698,159045837,173908417,206140930,3409108,SRX21223184,SRS18479986,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92088,,0.10596,,0.83295,,0.51602,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24735,SRR25492034,SRX21223184,SRS18479986,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR cut replicate S15,GSM7676110,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR cut replicate S15,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676110,GSM7676110: KBTGR cut replicate S15; Danio rerio; RNA Seq,GSM7676110 r1,GSM7676110,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTGRcut_S15_L002_I1_001.fastq.gz HYWGVBCXY_KBTGRcut_S15_L002_R1_001.fastq.gz HYWGVBCXY_KBTGRcut_S15_L002_R2_001.fastq.gz,fastq fastq fastq,960845292.0,7279131.0,GSM7676110 r8,0:8 1:26 2:98,A:207492886;C:148360000;G:162496060;T:194960451;N:45441,8,26,98,,207492886,148360000,162496060,194960451,45441,SRX21223184,SRS18479986,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92106,,0.10819,,0.82946,,0.51364,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24736,SRR25492037,SRX21223183,SRS18479987,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR cut replicate S14,GSM7676109,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR cut replicate S14,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676109,GSM7676109: KBTGR cut replicate S14; Danio rerio; RNA Seq,GSM7676109 r1,GSM7676109,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTGRcut_S14_L001_I1_001.fastq.gz H27K5BCX2_KBTGRcut_S14_L001_R1_001.fastq.gz H27K5BCX2_KBTGRcut_S14_L001_R2_001.fastq.gz,fastq fastq fastq,2591037900.0,19629075.0,GSM7676109 r1,0:8 1:26 2:98,A:555580990;C:402990210;G:441965039;T:522520043;N:593068,8,26,98,,555580990,402990210,441965039,522520043,593068,SRX21223183,SRS18479987,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92241,,0.10605,,0.83187,,0.51181,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24737,SRR25492038,SRX21223183,SRS18479987,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR cut replicate S14,GSM7676109,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR cut replicate S14,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676109,GSM7676109: KBTGR cut replicate S14; Danio rerio; RNA Seq,GSM7676109 r1,GSM7676109,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTGRcut_S14_L001_I1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S14_L001_R1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S14_L001_R2_001.fastq.gz,fastq fastq fastq,2497809996.0,18922803.0,GSM7676109 r2,0:8 1:26 2:98,A:535857014;C:388641161;G:426148721;T:502295548;N:1492250,8,26,98,,535857014,388641161,426148721,502295548,1492250,SRX21223183,SRS18479987,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92376,,0.10611,,0.83177,,0.49598,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24738,SRR25492039,SRX21223183,SRS18479987,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR cut replicate S14,GSM7676109,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR cut replicate S14,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676109,GSM7676109: KBTGR cut replicate S14; Danio rerio; RNA Seq,GSM7676109 r1,GSM7676109,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTGRcut_S14_L001_I1_001.fastq.gz HYLGMBCXY_KBTGRcut_S14_L001_R1_001.fastq.gz HYLGMBCXY_KBTGRcut_S14_L001_R2_001.fastq.gz,fastq fastq fastq,2728654500.0,20671625.0,GSM7676109 r3,0:8 1:26 2:98,A:584168882;C:423983386;G:464567203;T:543992364;N:9107415,8,26,98,,584168882,423983386,464567203,543992364,9107415,SRX21223183,SRS18479987,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92388,,0.10372,,0.83181,,0.50245,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24739,SRR25492040,SRX21223183,SRS18479987,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR cut replicate S14,GSM7676109,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR cut replicate S14,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676109,GSM7676109: KBTGR cut replicate S14; Danio rerio; RNA Seq,GSM7676109 r1,GSM7676109,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTGRcut_S14_L001_I1_001.fastq.gz HYWGVBCXY_KBTGRcut_S14_L001_R1_001.fastq.gz HYWGVBCXY_KBTGRcut_S14_L001_R2_001.fastq.gz,fastq fastq fastq,2618092488.0,19834034.0,GSM7676109 r4,0:8 1:26 2:98,A:561803683;C:406792207;G:446399294;T:528347486;N:392662,8,26,98,,561803683,406792207,446399294,528347486,392662,SRX21223183,SRS18479987,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92126,,0.10547,,0.83161,,0.49641,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24740,SRR25492041,SRX21223183,SRS18479987,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR cut replicate S14,GSM7676109,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR cut replicate S14,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676109,GSM7676109: KBTGR cut replicate S14; Danio rerio; RNA Seq,GSM7676109 r1,GSM7676109,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTGRcut_S14_L002_I1_001.fastq.gz H27K5BCX2_KBTGRcut_S14_L002_R1_001.fastq.gz H27K5BCX2_KBTGRcut_S14_L002_R2_001.fastq.gz,fastq fastq fastq,2564163096.0,19425478.0,GSM7676109 r5,0:8 1:26 2:98,A:549889204;C:398857562;G:437417974;T:517052381;N:479723,8,26,98,,549889204,398857562,437417974,517052381,479723,SRX21223183,SRS18479987,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.9232,,0.1061,,0.83071,,0.50282,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24741,SRR25492042,SRX21223183,SRS18479987,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR cut replicate S14,GSM7676109,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR cut replicate S14,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676109,GSM7676109: KBTGR cut replicate S14; Danio rerio; RNA Seq,GSM7676109 r1,GSM7676109,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTGRcut_S14_L002_I1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S14_L002_R1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S14_L002_R2_001.fastq.gz,fastq fastq fastq,2415052992.0,18295856.0,GSM7676109 r6,0:8 1:26 2:98,A:517947164;C:375865420;G:412233894;T:485594270;N:1353140,8,26,98,,517947164,375865420,412233894,485594270,1353140,SRX21223183,SRS18479987,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92288,,0.10488,,0.82899,,0.4957,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24742,SRR25492043,SRX21223183,SRS18479987,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR cut replicate S14,GSM7676109,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR cut replicate S14,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676109,GSM7676109: KBTGR cut replicate S14; Danio rerio; RNA Seq,GSM7676109 r1,GSM7676109,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTGRcut_S14_L002_I1_001.fastq.gz HYLGMBCXY_KBTGRcut_S14_L002_R1_001.fastq.gz HYLGMBCXY_KBTGRcut_S14_L002_R2_001.fastq.gz,fastq fastq fastq,2694434160.0,20412380.0,GSM7676109 r7,0:8 1:26 2:98,A:576891044;C:418621857;G:458706495;T:537348616;N:8845228,8,26,98,,576891044,418621857,458706495,537348616,8845228,SRX21223183,SRS18479987,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.9222,,0.10385,,0.83114,,0.50871,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24743,SRR25492044,SRX21223183,SRS18479987,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR cut replicate S14,GSM7676109,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR cut replicate S14,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676109,GSM7676109: KBTGR cut replicate S14; Danio rerio; RNA Seq,GSM7676109 r1,GSM7676109,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTGRcut_S14_L002_I1_001.fastq.gz HYWGVBCXY_KBTGRcut_S14_L002_R1_001.fastq.gz HYWGVBCXY_KBTGRcut_S14_L002_R2_001.fastq.gz,fastq fastq fastq,2615928216.0,19817638.0,GSM7676109 r8,0:8 1:26 2:98,A:561516458;C:406357695;G:445851758;T:528279876;N:122737,8,26,98,,561516458,406357695,445851758,528279876,122737,SRX21223183,SRS18479987,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92228,,0.10465,,0.8297,,0.49948,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24744,SRR25492045,SRX21223182,SRS18479985,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE normal replicate S4,GSM7676123,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE normal replicate S4,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676123,GSM7676123: KBTRE normal replicate S4; Danio rerio; RNA Seq,GSM7676123 r1,GSM7676123,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTREnormal_S4_L001_I1_001.fastq.gz H27K5BCX2_KBTREnormal_S4_L001_R1_001.fastq.gz H27K5BCX2_KBTREnormal_S4_L001_R2_001.fastq.gz,fastq fastq fastq,913827948.0,6922939.0,GSM7676123 r1,0:8 1:26 2:98,A:194246771;C:142826017;G:158206076;T:182961324;N:207834,8,26,98,,194246771,142826017,158206076,182961324,207834,SRX21223182,SRS18479985,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92133,,0.08495,,0.8536,,0.45396,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24745,SRR25492046,SRX21223182,SRS18479985,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE normal replicate S4,GSM7676123,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE normal replicate S4,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676123,GSM7676123: KBTRE normal replicate S4; Danio rerio; RNA Seq,GSM7676123 r1,GSM7676123,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTREnormal_S4_L001_I1_001.fastq.gz HFJ5GBCX2_KBTREnormal_S4_L001_R1_001.fastq.gz HFJ5GBCX2_KBTREnormal_S4_L001_R2_001.fastq.gz,fastq fastq fastq,882992616.0,6689338.0,GSM7676123 r2,0:8 1:26 2:98,A:187772330;C:137974909;G:152936254;T:176347715;N:523916,8,26,98,,187772330,137974909,152936254,176347715,523916,SRX21223182,SRS18479985,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.9217,,0.08483,,0.85271,,0.47289,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24746,SRR25492047,SRX21223182,SRS18479985,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE normal replicate S4,GSM7676123,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE normal replicate S4,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676123,GSM7676123: KBTRE normal replicate S4; Danio rerio; RNA Seq,GSM7676123 r1,GSM7676123,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTREnormal_S4_L001_I1_001.fastq.gz HYLGMBCXY_KBTREnormal_S4_L001_R1_001.fastq.gz HYLGMBCXY_KBTREnormal_S4_L001_R2_001.fastq.gz,fastq fastq fastq,960465132.0,7276251.0,GSM7676123 r3,0:8 1:26 2:98,A:203538013;C:149987509;G:166162505;T:190186167;N:3198404,8,26,98,,203538013,149987509,166162505,190186167,3198404,SRX21223182,SRS18479985,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92267,,0.08276,,0.85622,,0.45247,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures 24747,SRR25492048,SRX21223182,SRS18479985,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE normal replicate S4,GSM7676123,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE normal replicate S4,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676123,GSM7676123: KBTRE normal replicate S4; Danio rerio; RNA Seq,GSM7676123 r1,GSM7676123,1,For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTREnormal_S4_L001_I1_001.fastq.gz HYWGVBCXY_KBTREnormal_S4_L001_R1_001.fastq.gz HYWGVBCXY_KBTREnormal_S4_L001_R2_001.fastq.gz,fastq fastq fastq,913660704.0,6921672.0,GSM7676123 r4,0:8 1:26 2:98,A:194180593;C:142678595;G:158195155;T:183124445;N:145068,8,26,98,,194180593,142678595,158195155,183124445,145068,SRX21223182,SRS18479985,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92245,,0.08535,,0.85449,,0.45279,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures