{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"cDNA\", experiment.platform = \"ILLUMINA\" and technology = \"10x\"", "rows": [[9166, "ERR2788341", "ERX2797590", "ERS2709706", "ERP110806", "PRJEB28589", "Single cell transcriptional analysis reveals ILC like cells in zebrafish", "E-MTAB-7159", "Transcriptome Analysis", "Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.", "ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11", null, "Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 \uf06dl 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/\u03bcl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium\u2122 Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min  85\u00b0C for 5 min  held at 4\u00b0C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98\u00b0C for 3 min  12 cycles of 90\u00b0C for 15 s  67\u00b0C for 20 s and 72\u00b0C for 1 min  72\u00b0C for 1 min  held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min  65\u00b0C for 30 min  held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.", "5149STDY7292228", "SAMEA4890710", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK", "ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890710|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7292228|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP|individual:pool 4|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7292228|scientific name:Danio rerio|sex:2 female  1 male|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish", "E MTAB 7159:5149STDY7292228 p", "5149STDY7292228 p", "Single cell transcriptional analysis reveals ILC like cells in zebrafish", "The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 \uf06dl 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/\u03bcl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium\u2122 Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min  85\u00b0C for 5 min  held at 4\u00b0C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98\u00b0C for 3 min  12 cycles of 90\u00b0C for 15 s  67\u00b0C for 20 s and 72\u00b0C for 1 min  72\u00b0C for 1 min  held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min  65\u00b0C for 30 min  held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.", "Experimental Factor: genotype:Tglck:EGFP|Experimental Factor: infect:n1", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP110806", "Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish", "ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL", "5149STDY7292228.bam 5149STDY7292228.bam.bai", "bam bam", 37970494940.0, 387454030.0, "E MTAB 7159:5149STDY7292228", "0:98", "A:11476520187;C:7571635167;G:8189594199;T:10701044279;N:31701108", 98, null, null, null, 11476520187, 7571635167, 8189594199, 10701044279, 31701108, "ERX2797590", "ERS2709706", "ERA1594569", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", 1, 0.87568, null, 0.2122, null, 0.82582, null, 0.5259, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2018-09-11", "Adult", "Adult", "Gut", "Digestive System"], [9167, "ERR2788340", "ERX2797589", "ERS2709705", "ERP110806", "PRJEB28589", "Single cell transcriptional analysis reveals ILC like cells in zebrafish", "E-MTAB-7159", "Transcriptome Analysis", "Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.", "ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11", null, "Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 \uf06dl 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/\u03bcl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium\u2122 Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min  85\u00b0C for 5 min  held at 4\u00b0C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98\u00b0C for 3 min  12 cycles of 90\u00b0C for 15 s  67\u00b0C for 20 s and 72\u00b0C for 1 min  72\u00b0C for 1 min  held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min  65\u00b0C for 30 min  held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.", "5149STDY7274848", "SAMEA4890709", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK", "ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890709|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274848|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 3|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274848|scientific name:Danio rerio|sex:female|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish", "E MTAB 7159:5149STDY7274848 p", "5149STDY7274848 p", "Single cell transcriptional analysis reveals ILC like cells in zebrafish", "The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 \uf06dl 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/\u03bcl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium\u2122 Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min  85\u00b0C for 5 min  held at 4\u00b0C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98\u00b0C for 3 min  12 cycles of 90\u00b0C for 15 s  67\u00b0C for 20 s and 72\u00b0C for 1 min  72\u00b0C for 1 min  held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min  65\u00b0C for 30 min  held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.", "Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:Vibrio Anguillarum", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP110806", "Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish", "ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL", "5149STDY7274848.bam 5149STDY7274848.bam.bai", "bam bam", 34517322840.0, 352217580.0, "E MTAB 7159:5149STDY7274848", "0:98", "A:10635243399;C:6658515314;G:7525079510;T:9695995344;N:2489273", 98, null, null, null, 10635243399, 6658515314, 7525079510, 9695995344, 2489273, "ERX2797589", "ERS2709705", "ERA1594569", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", 1, 0.86206, null, 0.18065, null, 0.83514, null, 0.53609, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2018-09-11", "Adult", "Adult", "Gut", "Digestive System"], [9168, "ERR2788339", "ERX2797588", "ERS2709704", "ERP110806", "PRJEB28589", "Single cell transcriptional analysis reveals ILC like cells in zebrafish", "E-MTAB-7159", "Transcriptome Analysis", "Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.", "ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11", null, "Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 \uf06dl 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/\u03bcl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium\u2122 Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min  85\u00b0C for 5 min  held at 4\u00b0C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98\u00b0C for 3 min  12 cycles of 90\u00b0C for 15 s  67\u00b0C for 20 s and 72\u00b0C for 1 min  72\u00b0C for 1 min  held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min  65\u00b0C for 30 min  held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.", "5149STDY7274847", "SAMEA4890708", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK", "ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890708|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274847|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 2|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274847|scientific name:Danio rerio|sex:female|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish", "E MTAB 7159:5149STDY7274847 p", "5149STDY7274847 p", "Single cell transcriptional analysis reveals ILC like cells in zebrafish", "The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 \uf06dl 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/\u03bcl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium\u2122 Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min  85\u00b0C for 5 min  held at 4\u00b0C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98\u00b0C for 3 min  12 cycles of 90\u00b0C for 15 s  67\u00b0C for 20 s and 72\u00b0C for 1 min  72\u00b0C for 1 min  held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min  65\u00b0C for 30 min  held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.", "Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:Anisakis simplex", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP110806", "Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish", "ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL", "5149STDY7274847.bam 5149STDY7274847.bam.bai", "bam bam", 34467649678.0, 351710711.0, "E MTAB 7159:5149STDY7274847", "0:98", "A:10609988948;C:6722093635;G:7464497879;T:9667814950;N:3254266", 98, null, null, null, 10609988948, 6722093635, 7464497879, 9667814950, 3254266, "ERX2797588", "ERS2709704", "ERA1594569", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", 1, 0.88751, null, 0.21835, null, 0.83771, null, 0.53927, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2018-09-11", "Adult", "Adult", "Gut", "Digestive System"], [9169, "ERR2788338", "ERX2797587", "ERS2709703", "ERP110806", "PRJEB28589", "Single cell transcriptional analysis reveals ILC like cells in zebrafish", "E-MTAB-7159", "Transcriptome Analysis", "Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.", "ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11", null, "Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 \uf06dl 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/\u03bcl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium\u2122 Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min  85\u00b0C for 5 min  held at 4\u00b0C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98\u00b0C for 3 min  12 cycles of 90\u00b0C for 15 s  67\u00b0C for 20 s and 72\u00b0C for 1 min  72\u00b0C for 1 min  held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min  65\u00b0C for 30 min  held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.", "5149STDY7274846", "SAMEA4890707", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK", "ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890707|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274846|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 1|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274846|scientific name:Danio rerio|sex:female|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish", "E MTAB 7159:5149STDY7274846 p", "5149STDY7274846 p", "Single cell transcriptional analysis reveals ILC like cells in zebrafish", "The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 \uf06dl 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/\u03bcl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium\u2122 Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min  85\u00b0C for 5 min  held at 4\u00b0C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98\u00b0C for 3 min  12 cycles of 90\u00b0C for 15 s  67\u00b0C for 20 s and 72\u00b0C for 1 min  72\u00b0C for 1 min  held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min  65\u00b0C for 30 min  held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.", "Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:n1", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP110806", "Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish", "ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL", "5149STDY7274846.bam 5149STDY7274846.bam.bai", "bam bam", 35052538472.0, 357678964.0, "E MTAB 7159:5149STDY7274846", "0:98", "A:10698116265;C:6858102477;G:7626019661;T:9866905792;N:3394277", 98, null, null, null, 10698116265, 6858102477, 7626019661, 9866905792, 3394277, "ERX2797587", "ERS2709703", "ERA1594569", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", 1, 0.88916, null, 0.21537, null, 0.83802, null, 0.5336, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2018-09-11", "Adult", "Adult", "Gut", "Digestive System"], [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.", null, null, null, "KBTRE  cut  replicate S12", "GSM7676118", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.11469, null, 0.85372, null, 0.50388, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  cut  replicate S12", "GSM7676118", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.11373, null, 0.85226, null, 0.50246, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  cut  replicate S12", "GSM7676118", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.11168, null, 0.85245, null, 0.5097, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  cut  replicate S12", "GSM7676118", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.11383, null, 0.85212, null, 0.49917, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  cut  replicate S12", "GSM7676118", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.11359, null, 0.85307, null, 0.49119, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  cut  replicate S12", "GSM7676118", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.11494, null, 0.85378, null, 0.48986, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  cut  replicate S12", "GSM7676118", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.11027, null, 0.85354, null, 0.50421, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  cut  replicate S12", "GSM7676118", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.11379, null, 0.85346, null, 0.50695, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  cut  replicate S10", "GSM7676116", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.11493, null, 0.85719, null, 0.50794, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  cut  replicate S10", "GSM7676116", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.11588, null, 0.85415, null, 0.50804, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  cut  replicate S10", "GSM7676116", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.11262, null, 0.8561, null, 0.49742, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  cut  replicate S10", "GSM7676116", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.11332, null, 0.85401, null, 0.51062, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  cut  replicate S10", "GSM7676116", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.11301, null, 0.85449, null, 0.50422, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  cut  replicate S10", "GSM7676116", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.11377, null, 0.8548, null, 0.50065, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  cut  replicate S10", "GSM7676116", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.11551, null, 0.85634, null, 0.50392, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  cut  replicate S10", "GSM7676116", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.11506, null, 0.85504, null, 0.49763, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  cut  replicate S11", "GSM7676117", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.1155, null, 0.85283, null, 0.5061, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  cut  replicate S11", "GSM7676117", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.11485, null, 0.85429, null, 0.49592, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  cut  replicate S11", "GSM7676117", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.1132, null, 0.8537, null, 0.50609, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  cut  replicate S11", "GSM7676117", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.1139, null, 0.85307, null, 0.50536, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  cut  replicate S11", "GSM7676117", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.11403, null, 0.85267, null, 0.50361, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  cut  replicate S11", "GSM7676117", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.11265, null, 0.85273, null, 0.49392, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  cut  replicate S11", "GSM7676117", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.11108, null, 0.85449, null, 0.48271, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  cut  replicate S11", "GSM7676117", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.11279, null, 0.85212, null, 0.49708, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S8", "GSM7676115", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09159, null, 0.82191, null, 0.48306, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S8", "GSM7676115", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09205, null, 0.82039, null, 0.48039, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S8", "GSM7676115", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.08941, null, 0.82331, null, 0.49215, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S8", "GSM7676115", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09192, null, 0.82229, null, 0.49666, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S8", "GSM7676115", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09211, null, 0.82207, null, 0.48301, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S8", "GSM7676115", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09094, null, 0.82189, null, 0.47933, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S8", "GSM7676115", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09059, null, 0.82345, null, 0.49626, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S8", "GSM7676115", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09144, null, 0.82089, null, 0.49057, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S7", "GSM7676114", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.0948, null, 0.82576, null, 0.48767, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S7", "GSM7676114", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09445, null, 0.82319, null, 0.49095, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S7", "GSM7676114", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09165, null, 0.82432, null, 0.48843, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S7", "GSM7676114", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09294, null, 0.82304, null, 0.48936, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S7", "GSM7676114", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09291, null, 0.82513, null, 0.48834, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S7", "GSM7676114", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09237, null, 0.8244, null, 0.48574, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S7", "GSM7676114", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09019, null, 0.82696, null, 0.4934, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S7", "GSM7676114", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.0929, null, 0.82507, null, 0.48822, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S6", "GSM7676113", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09178, null, 0.82089, null, 0.49952, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S6", "GSM7676113", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09263, null, 0.82016, null, 0.49849, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S6", "GSM7676113", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09037, null, 0.82339, null, 0.49743, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S6", "GSM7676113", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09131, null, 0.82193, null, 0.49736, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S6", "GSM7676113", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09211, null, 0.82069, null, 0.49043, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S6", "GSM7676113", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09174, null, 0.82152, null, 0.48524, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S6", "GSM7676113", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.08938, null, 0.82189, null, 0.49517, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S6", "GSM7676113", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09105, null, 0.82142, null, 0.48867, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S5", "GSM7676112", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09296, null, 0.82288, null, 0.48038, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S5", "GSM7676112", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09356, null, 0.82386, null, 0.4736, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S5", "GSM7676112", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09118, null, 0.82513, null, 0.48007, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S5", "GSM7676112", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09327, null, 0.82221, null, 0.47626, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S5", "GSM7676112", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09295, null, 0.82333, null, 0.48441, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S5", "GSM7676112", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09407, null, 0.82225, null, 0.47898, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S5", "GSM7676112", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09153, null, 0.82386, null, 0.48775, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  normal  replicate S5", "GSM7676112", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.09341, null, 0.82211, null, 0.49121, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  cut  replicate S16", "GSM7676111", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.10972, null, 0.83684, null, 0.49054, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  cut  replicate S16", "GSM7676111", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.11044, null, 0.83593, null, 0.49929, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  cut  replicate S16", "GSM7676111", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.1075, null, 0.83733, null, 0.49995, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  cut  replicate S16", "GSM7676111", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.10934, null, 0.83583, null, 0.5109, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  cut  replicate S16", "GSM7676111", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.10865, null, 0.83771, null, 0.4962, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  cut  replicate S16", "GSM7676111", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.11008, null, 0.83252, null, 0.48566, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  cut  replicate S16", "GSM7676111", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.10681, null, 0.83727, null, 0.49306, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  cut  replicate S16", "GSM7676111", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.1079, null, 0.83465, null, 0.49184, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  normal  replicate S2", "GSM7676121", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.08811, null, 0.85433, null, 0.4736, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  normal  replicate S2", "GSM7676121", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.08644, null, 0.85464, null, 0.47495, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  normal  replicate S2", "GSM7676121", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.08441, null, 0.85681, null, 0.45235, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  normal  replicate S2", "GSM7676121", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.08698, null, 0.85626, null, 0.47803, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  normal  replicate S2", "GSM7676121", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.08446, null, 0.85685, null, 0.47524, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  normal  replicate S2", "GSM7676121", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.08593, null, 0.85529, null, 0.47658, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  normal  replicate S2", "GSM7676121", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.08693, null, 0.85689, null, 0.45239, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  normal  replicate S2", "GSM7676121", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.086, null, 0.85752, null, 0.46487, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  cut  replicate S15", "GSM7676110", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.10915, null, 0.83163, null, 0.51061, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  cut  replicate S15", "GSM7676110", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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. 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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.", null, null, null, "KBTGR  cut  replicate S15", "GSM7676110", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.10509, null, 0.83179, null, 0.5158, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  cut  replicate S15", "GSM7676110", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.10724, null, 0.83031, null, 0.51032, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  cut  replicate S15", "GSM7676110", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.10822, null, 0.83078, null, 0.51544, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  cut  replicate S15", "GSM7676110", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.10759, null, 0.83142, null, 0.51632, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  cut  replicate S15", "GSM7676110", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.10596, null, 0.83295, null, 0.51602, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  cut  replicate S15", "GSM7676110", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.10819, null, 0.82946, null, 0.51364, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  cut  replicate S14", "GSM7676109", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.10605, null, 0.83187, null, 0.51181, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  cut  replicate S14", "GSM7676109", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.10611, null, 0.83177, null, 0.49598, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  cut  replicate S14", "GSM7676109", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.10372, null, 0.83181, null, 0.50245, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  cut  replicate S14", "GSM7676109", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.10547, null, 0.83161, null, 0.49641, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  cut  replicate S14", "GSM7676109", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.1061, null, 0.83071, null, 0.50282, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  cut  replicate S14", "GSM7676109", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.10488, null, 0.82899, null, 0.4957, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  cut  replicate S14", "GSM7676109", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.10385, null, 0.83114, null, 0.50871, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTGR  cut  replicate S14", "GSM7676109", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.10465, null, 0.8297, null, 0.49948, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  normal  replicate S4", "GSM7676123", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.08495, null, 0.8536, null, 0.45396, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  normal  replicate S4", "GSM7676123", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.08483, null, 0.85271, null, 0.47289, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  normal  replicate S4", "GSM7676123", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.08276, null, 0.85622, null, 0.45247, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "KBTRE  normal  replicate S4", "GSM7676123", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP452960", null, "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, null, 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, null, 0.08535, null, 0.85449, null, 0.45279, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_droplet", "10x", null, "Chile", "2023-08-02", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [24748, "SRR25492049", "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.", null, null, null, "KBTRE  normal  replicate S4", "GSM7676123", null, "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", null, "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 \u00b5m 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\u2019 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.", null, "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 \u00b5m 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. 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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. 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