metadata: run_metadata: 1,001 rows where devstage_curation = "Undetermined" and technology = "10x"

1,001 rows where devstage_curation = "Undetermined" and technology = "10x"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
11777	11777	ERR11758595	ERX11157718	ERS16172936	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl tb	SAMEA114192243	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192243\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl tb\|age:10\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:tail bud prominent stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl tb\|scientific name:Danio rerio\|strain:drl:H2B Dendra2							Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl tb p	drl tb p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_tb_S36_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S36_L001_R1_001.fastq.gz	fastq fastq	211593816.0	1679316.0	E MTAB 13196:drl h2b dendra tb S36 L001	0:28 1:98	A:62689430;C:45809168;G:45709128;T:57272091;N:113999	28	98		62689430	45809168	45709128	57272091	113999	ERX11157718	ERS16172936	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00192	0.91331	0.00072	0.14588	0.99675	0.89292	0.51304	0.63144	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
11778	11778	ERR11758629	ERX11157718	ERS16172936	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl tb	SAMEA114192243	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192243\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl tb\|age:10\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:tail bud prominent stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl tb\|scientific name:Danio rerio\|strain:drl:H2B Dendra2							Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl tb p	drl tb p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_tb_S37_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S37_L001_R1_001.fastq.gz	fastq fastq	980164836.0	7779086.0	E MTAB 13196:drl h2b dendra tb S37 L001	0:28 1:98	A:281375011;C:216067640;G:222839674;T:259781180;N:101331	28	98		281375011	216067640	222839674	259781180	101331	ERX11157718	ERS16172936	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00817	0.89718	0.00237	0.12153	0.98912	0.82643	0.46403	0.64954	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
11779	11779	ERR11758618	ERX11157718	ERS16172936	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl tb	SAMEA114192243	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192243\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl tb\|age:10\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:tail bud prominent stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl tb\|scientific name:Danio rerio\|strain:drl:H2B Dendra2							Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl tb p	drl tb p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_tb_S39_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S39_L001_R1_001.fastq.gz	fastq fastq	12118302.0	96177.0	E MTAB 13196:drl h2b dendra tb S39 L001	0:28 1:98	A:3543790;C:2662872;G:2728134;T:3182383;N:1123	28	98		3543790	2662872	2728134	3182383	1123	ERX11157718	ERS16172936	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00786	0.88963	0.0025	0.12543	0.99403	0.88635	0.50098	0.64694	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
11780	11780	ERR11758643	ERX11157718	ERS16172936	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl tb	SAMEA114192243	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192243\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl tb\|age:10\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:tail bud prominent stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl tb\|scientific name:Danio rerio\|strain:drl:H2B Dendra2							Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl tb p	drl tb p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_tb_S5_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S5_L005_R1_001.fastq.gz	fastq fastq	2061022698.0	16357323.0	E MTAB 13196:drl h2b dendra tb S5 L005	0:28 1:98	A:587730953;C:457631700;G:470283474;T:545196979;N:179592	28	98		587730953	457631700	470283474	545196979	179592	ERX11157718	ERS16172936	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.01192	0.91661	0.00336	0.12397	0.98518	0.82568	0.45692	0.65555	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
11781	11781	ERR11758610	ERX11157718	ERS16172936	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl tb	SAMEA114192243	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192243\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl tb\|age:10\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:tail bud prominent stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl tb\|scientific name:Danio rerio\|strain:drl:H2B Dendra2							Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl tb p	drl tb p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_tb_S38_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S38_L001_R1_001.fastq.gz	fastq fastq	924603120.0	7338120.0	E MTAB 13196:drl h2b dendra tb S38 L001	0:28 1:98	A:265987815;C:203824483;G:210024160;T:244670646;N:96016	28	98		265987815	203824483	210024160	244670646	96016	ERX11157718	ERS16172936	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00773	0.89881	0.00242	0.12145	0.98944	0.82948	0.50529	0.66568	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
11782	11782	ERR11758641	ERX11157718	ERS16172936	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl tb	SAMEA114192243	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192243\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl tb\|age:10\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:tail bud prominent stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl tb\|scientific name:Danio rerio\|strain:drl:H2B Dendra2							Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl tb p	drl tb p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_tb_S6_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S6_L005_R1_001.fastq.gz	fastq fastq	1954661562.0	15513187.0	E MTAB 13196:drl h2b dendra tb S6 L005	0:28 1:98	A:558769608;C:433724557;G:445550100;T:516443984;N:173313	28	98		558769608	433724557	445550100	516443984	173313	ERX11157718	ERS16172936	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.0125	0.91697	0.00373	0.12359	0.98447	0.82558	0.4881	0.6456	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
11783	11783	ERR11758591	ERX11157718	ERS16172936	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl tb	SAMEA114192243	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192243\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl tb\|age:10\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:tail bud prominent stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl tb\|scientific name:Danio rerio\|strain:drl:H2B Dendra2							Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl tb p	drl tb p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_tb_S35_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S35_L001_R1_001.fastq.gz	fastq fastq	4717188.0	37438.0	E MTAB 13196:drl h2b dendra tb S35 L001	0:28 1:98	A:1419430;C:1014265;G:1016661;T:1264642;N:2190	28	98		1419430	1014265	1016661	1264642	2190	ERX11157718	ERS16172936	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.0012	0.65482	0.00054	0.10783	0.99953	0.97157	0.625	0.63689	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
11784	11784	ERR11758606	ERX11157718	ERS16172936	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl tb	SAMEA114192243	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192243\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl tb\|age:10\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:tail bud prominent stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl tb\|scientific name:Danio rerio\|strain:drl:H2B Dendra2							Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl tb p	drl tb p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_tb_S34_L001_R1_001.fastq.gz drl_h2b-dendra_tb_S34_L001_R2_001.fastq.gz	fastq fastq	303645636.0	2409886.0	E MTAB 13196:drl h2b dendra tb S34 L001	0:28 1:98	A:90748559;C:65369482;G:65969002;T:81405258;N:153335	28	98		90748559	65369482	65969002	81405258	153335	ERX11157718	ERS16172936	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00228	0.91262	0.00099	0.14666	0.99638	0.89006	0.47177	0.63109	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
11785	11785	ERR11758640	ERX11157718	ERS16172936	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl tb	SAMEA114192243	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192243\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl tb\|age:10\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:tail bud prominent stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl tb\|scientific name:Danio rerio\|strain:drl:H2B Dendra2							Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl tb p	drl tb p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_tb_S40_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S40_L001_R1_001.fastq.gz	fastq fastq	661361022.0	5248897.0	E MTAB 13196:drl h2b dendra tb S40 L001	0:28 1:98	A:190087869;C:145985661;G:150124621;T:175095762;N:67109	28	98		190087869	145985661	150124621	175095762	67109	ERX11157718	ERS16172936	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00785	0.89784	0.00251	0.12159	0.98948	0.83055	0.46095	0.64951	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
11786	11786	ERR11758605	ERX11157718	ERS16172936	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl tb	SAMEA114192243	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192243\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl tb\|age:10\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:tail bud prominent stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl tb\|scientific name:Danio rerio\|strain:drl:H2B Dendra2							Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl tb p	drl tb p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_tb_S7_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S7_L005_R1_001.fastq.gz	fastq fastq	25157790.0	199665.0	E MTAB 13196:drl h2b dendra tb S7 L005	0:28 1:98	A:7330053;C:5600451;G:5635840;T:6589498;N:1948	28	98		7330053	5600451	5635840	6589498	1948	ERX11157718	ERS16172936	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.01201	0.91385	0.00341	0.12826	0.98595	0.85161	0.49226	0.64953	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
11787	11787	ERR11758600	ERX11157718	ERS16172936	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl tb	SAMEA114192243	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192243\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl tb\|age:10\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:tail bud prominent stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl tb\|scientific name:Danio rerio\|strain:drl:H2B Dendra2							Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl tb p	drl tb p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_tb_S8_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S8_L005_R1_001.fastq.gz	fastq fastq	1422735804.0	11291554.0	E MTAB 13196:drl h2b dendra tb S8 L005	0:28 1:98	A:405788442;C:317299433;G:322206476;T:377317416;N:124037	28	98		405788442	317299433	322206476	377317416	124037	ERX11157718	ERS16172936	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.01226	0.91547	0.0037	0.12565	0.9849	0.83662	0.48279	0.64531	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
11788	11788	ERR11758616	ERX11157718	ERS16172936	ERP149744	PRJEB64563	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E-MTAB-13196	Transcriptome Analysis	Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	drl tb	SAMEA114192243	Institute of Molecular Genetics of the Czech Academy of Sciences	ENA FIRST PUBLIC:2023 08 01T00:17:16Z\|ENA LAST UPDATE:2023 08 01T00:17:16Z\|External Id:SAMEA114192243\|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences\|INSDC first public:2023 08 01T00:17:16Z\|INSDC last update:2023 08 01T00:17:16Z\|INSDC status:public\|Submitter Id:E MTAB 13196:drl tb\|age:10\|broker name:ArrayExpress\|cell type:endothelial cell\|collection date:not collected\|common name:zebrafish\|developmental stage:tail bud prominent stage\|genotype:drl:H2B Dendra2\|geographic location country and/or sea:not collected\|immunophenotype:drl:H2B Dendra2+\|isolate:not applicable\|organism part:embryo\|sample name:E MTAB 13196:drl tb\|scientific name:Danio rerio\|strain:drl:H2B Dendra2							Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	E MTAB 13196:drl tb p	drl tb p	Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	ERP149744	Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos	ENA FIRST PUBLIC:2023 08 01\|ENA LAST UPDATE:2023 08 01	drl_h2b-dendra_tb_S33_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S33_L001_R1_001.fastq.gz	fastq fastq	328918212.0	2610462.0	E MTAB 13196:drl h2b dendra tb S33 L001	0:28 1:98	A:98036464;C:71090137;G:71650807;T:87969481;N:171323	28	98		98036464	71090137	71650807	87969481	171323	ERX11157718	ERS16172936	ERA25628220	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	Institute of Molecular Genetics of the Czech Academy of Sciences\|European Nucleotide Archive	2	0.00197	0.89969	0.00087	0.14269	0.99681	0.89134	0.49763	0.63651	28	98	T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	Czech Republic	2023-08-01	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
24656	24656	SRR25491963	SRX21223193	SRS18479996	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE cut replicate S12	GSM7676118		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE cut replicate S12	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676118	GSM7676118: KBTRE cut replicate S12; Danio rerio; RNA Seq	GSM7676118 r1	GSM7676118	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	H27K5BCX2_KBTREcut_S12_L001_R2_001.fastq.gz H27K5BCX2_KBTREcut_S12_L001_R1_001.fastq.gz H27K5BCX2_KBTREcut_S12_L001_I1_001.fastq.gz	fastq fastq fastq	664936140.0	5037395.0	GSM7676118 r1	0:8 1:26 2:98	A:143407233;C:100996340;G:110567290;T:138539687;N:154160	8	26	98	143407233	100996340	110567290	138539687	154160	SRX21223193	SRS18479996	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.91249		0.11469		0.85372		0.50388		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24657	24657	SRR25491964	SRX21223193	SRS18479996	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE cut replicate S12	GSM7676118		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE cut replicate S12	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676118	GSM7676118: KBTRE cut replicate S12; Danio rerio; RNA Seq	GSM7676118 r1	GSM7676118	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HFJ5GBCX2_KBTREcut_S12_L001_R2_001.fastq.gz HFJ5GBCX2_KBTREcut_S12_L001_R1_001.fastq.gz HFJ5GBCX2_KBTREcut_S12_L001_I1_001.fastq.gz	fastq fastq fastq	645128748.0	4887339.0	GSM7676118 r2	0:8 1:26 2:98	A:139238913;C:98013961;G:107274566;T:134050699;N:381083	8	26	98	139238913	98013961	107274566	134050699	381083	SRX21223193	SRS18479996	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.91125		0.11373		0.85226		0.50246		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24658	24658	SRR25491965	SRX21223193	SRS18479996	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE cut replicate S12	GSM7676118		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE cut replicate S12	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676118	GSM7676118: KBTRE cut replicate S12; Danio rerio; RNA Seq	GSM7676118 r1	GSM7676118	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYLGMBCXY_KBTREcut_S12_L001_I1_001.fastq.gz HYLGMBCXY_KBTREcut_S12_L001_R1_001.fastq.gz HYLGMBCXY_KBTREcut_S12_L001_R2_001.fastq.gz	fastq fastq fastq	701173044.0	5311917.0	GSM7676118 r3	0:8 1:26 2:98	A:151296425;C:106327416;G:116370981;T:144230427;N:2342617	8	26	98	151296425	106327416	116370981	144230427	2342617	SRX21223193	SRS18479996	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.91082		0.11168		0.85245		0.5097		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24659	24659	SRR25491966	SRX21223193	SRS18479996	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE cut replicate S12	GSM7676118		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE cut replicate S12	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676118	GSM7676118: KBTRE cut replicate S12; Danio rerio; RNA Seq	GSM7676118 r1	GSM7676118	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYWGVBCXY_KBTREcut_S12_L001_I1_001.fastq.gz HYWGVBCXY_KBTREcut_S12_L001_R1_001.fastq.gz HYWGVBCXY_KBTREcut_S12_L001_R2_001.fastq.gz	fastq fastq fastq	656204604.0	4971247.0	GSM7676118 r4	0:8 1:26 2:98	A:141756368;C:99522317;G:109015686;T:136785011;N:102824	8	26	98	141756368	99522317	109015686	136785011	102824	SRX21223193	SRS18479996	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.90953		0.11383		0.85212		0.49917		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24660	24660	SRR25492087	SRX21223193	SRS18479996	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE cut replicate S12	GSM7676118		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE cut replicate S12	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676118	GSM7676118: KBTRE cut replicate S12; Danio rerio; RNA Seq	GSM7676118 r1	GSM7676118	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	H27K5BCX2_KBTREcut_S12_L002_I1_001.fastq.gz H27K5BCX2_KBTREcut_S12_L002_R1_001.fastq.gz H27K5BCX2_KBTREcut_S12_L002_R2_001.fastq.gz	fastq fastq fastq	658691616.0	4990088.0	GSM7676118 r5	0:8 1:26 2:98	A:142071317;C:100089239;G:109564812;T:137176685;N:126571	8	26	98	142071317	100089239	109564812	137176685	126571	SRX21223193	SRS18479996	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.9118		0.11359		0.85307		0.49119		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24661	24661	SRR25492088	SRX21223193	SRS18479996	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE cut replicate S12	GSM7676118		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE cut replicate S12	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676118	GSM7676118: KBTRE cut replicate S12; Danio rerio; RNA Seq	GSM7676118 r1	GSM7676118	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HFJ5GBCX2_KBTREcut_S12_L002_I1_001.fastq.gz HFJ5GBCX2_KBTREcut_S12_L002_R1_001.fastq.gz HFJ5GBCX2_KBTREcut_S12_L002_R2_001.fastq.gz	fastq fastq fastq	626035872.0	4742696.0	GSM7676118 r6	0:8 1:26 2:98	A:135079818;C:95138940;G:104158101;T:130050700;N:356649	8	26	98	135079818	95138940	104158101	130050700	356649	SRX21223193	SRS18479996	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.9103		0.11494		0.85378		0.48986		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24662	24662	SRR25492089	SRX21223193	SRS18479996	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE cut replicate S12	GSM7676118		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE cut replicate S12	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676118	GSM7676118: KBTRE cut replicate S12; Danio rerio; RNA Seq	GSM7676118 r1	GSM7676118	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYLGMBCXY_KBTREcut_S12_L002_I1_001.fastq.gz HYLGMBCXY_KBTREcut_S12_L002_R1_001.fastq.gz HYLGMBCXY_KBTREcut_S12_L002_R2_001.fastq.gz	fastq fastq fastq	693479028.0	5253629.0	GSM7676118 r7	0:8 1:26 2:98	A:149676332;C:105134718;G:115079858;T:142696573;N:2268161	8	26	98	149676332	105134718	115079858	142696573	2268161	SRX21223193	SRS18479996	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.91107		0.11027		0.85354		0.50421		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24663	24663	SRR25492090	SRX21223193	SRS18479996	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE cut replicate S12	GSM7676118		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE cut replicate S12	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676118	GSM7676118: KBTRE cut replicate S12; Danio rerio; RNA Seq	GSM7676118 r1	GSM7676118	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYWGVBCXY_KBTREcut_S12_L002_R2_001.fastq.gz HYWGVBCXY_KBTREcut_S12_L002_R1_001.fastq.gz HYWGVBCXY_KBTREcut_S12_L002_I1_001.fastq.gz	fastq fastq fastq	656957664.0	4976952.0	GSM7676118 r8	0:8 1:26 2:98	A:141922523;C:99627529;G:109167065;T:136992486;N:31693	8	26	98	141922523	99627529	109167065	136992486	31693	SRX21223193	SRS18479996	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.91107		0.11379		0.85346		0.50695		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24664	24664	SRR25491967	SRX21223192	SRS18479995	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE cut replicate S10	GSM7676116		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE cut replicate S10	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676116	GSM7676116: KBTRE cut replicate S10; Danio rerio; RNA Seq	GSM7676116 r1	GSM7676116	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	H27K5BCX2_KBTREcut_S10_L001_R2_001.fastq.gz H27K5BCX2_KBTREcut_S10_L001_R1_001.fastq.gz H27K5BCX2_KBTREcut_S10_L001_I1_001.fastq.gz	fastq fastq fastq	1062185256.0	8046858.0	GSM7676116 r1	0:8 1:26 2:98	A:230014489;C:161623855;G:176773666;T:219935294;N:244780	8	26	98	230014489	161623855	176773666	219935294	244780	SRX21223192	SRS18479995	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.91294		0.11493		0.85719		0.50794		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24665	24665	SRR25491968	SRX21223192	SRS18479995	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE cut replicate S10	GSM7676116		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE cut replicate S10	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676116	GSM7676116: KBTRE cut replicate S10; Danio rerio; RNA Seq	GSM7676116 r1	GSM7676116	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HFJ5GBCX2_KBTREcut_S10_L001_R2_001.fastq.gz HFJ5GBCX2_KBTREcut_S10_L001_R1_001.fastq.gz HFJ5GBCX2_KBTREcut_S10_L001_I1_001.fastq.gz	fastq fastq fastq	1034539308.0	7837419.0	GSM7676116 r2	0:8 1:26 2:98	A:224616171;C:157304961;G:172084243;T:213455656;N:606031	8	26	98	224616171	157304961	172084243	213455656	606031	SRX21223192	SRS18479995	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.91287		0.11588		0.85415		0.50804		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24666	24666	SRR25491969	SRX21223192	SRS18479995	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE cut replicate S10	GSM7676116		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE cut replicate S10	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676116	GSM7676116: KBTRE cut replicate S10; Danio rerio; RNA Seq	GSM7676116 r1	GSM7676116	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYLGMBCXY_KBTREcut_S10_L001_R2_001.fastq.gz HYLGMBCXY_KBTREcut_S10_L001_R1_001.fastq.gz HYLGMBCXY_KBTREcut_S10_L001_I1_001.fastq.gz	fastq fastq fastq	1122858660.0	8506505.0	GSM7676116 r3	0:8 1:26 2:98	A:243355100;C:170483208;G:186449194;T:229601473;N:3748515	8	26	98	243355100	170483208	186449194	229601473	3748515	SRX21223192	SRS18479995	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.91213		0.11262		0.8561		0.49742		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24667	24667	SRR25491970	SRX21223192	SRS18479995	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE cut replicate S10	GSM7676116		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE cut replicate S10	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676116	GSM7676116: KBTRE cut replicate S10; Danio rerio; RNA Seq	GSM7676116 r1	GSM7676116	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYWGVBCXY_KBTREcut_S10_L001_I1_001.fastq.gz HYWGVBCXY_KBTREcut_S10_L001_R1_001.fastq.gz HYWGVBCXY_KBTREcut_S10_L001_R2_001.fastq.gz	fastq fastq fastq	1044506496.0	7912928.0	GSM7676116 r4	0:8 1:26 2:98	A:226413586;C:158757664;G:173768785;T:216364905;N:162004	8	26	98	226413586	158757664	173768785	216364905	162004	SRX21223192	SRS18479995	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.9121		0.11332		0.85401		0.51062		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24668	24668	SRR25491971	SRX21223192	SRS18479995	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE cut replicate S10	GSM7676116		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE cut replicate S10	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676116	GSM7676116: KBTRE cut replicate S10; Danio rerio; RNA Seq	GSM7676116 r1	GSM7676116	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYLGMBCXY_KBTREcut_S10_L002_I1_001.fastq.gz HYLGMBCXY_KBTREcut_S10_L002_R1_001.fastq.gz HYLGMBCXY_KBTREcut_S10_L002_R2_001.fastq.gz	fastq fastq fastq	1110246720.0	8410960.0	GSM7676116 r7	0:8 1:26 2:98	A:240787456;C:168521971;G:184254856;T:227029149;N:3680648	8	26	98	240787456	168521971	184254856	227029149	3680648	SRX21223192	SRS18479995	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.91246		0.11301		0.85449		0.50422		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24669	24669	SRR25491972	SRX21223192	SRS18479995	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE cut replicate S10	GSM7676116		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE cut replicate S10	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676116	GSM7676116: KBTRE cut replicate S10; Danio rerio; RNA Seq	GSM7676116 r1	GSM7676116	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYWGVBCXY_KBTREcut_S10_L002_I1_001.fastq.gz HYWGVBCXY_KBTREcut_S10_L002_R1_001.fastq.gz HYWGVBCXY_KBTREcut_S10_L002_R2_001.fastq.gz	fastq fastq fastq	1046026740.0	7924445.0	GSM7676116 r8	0:8 1:26 2:98	A:226911006;C:158976256;G:173939936;T:216718492;N:49920	8	26	98	226911006	158976256	173939936	216718492	49920	SRX21223192	SRS18479995	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.91267		0.11377		0.8548		0.50065		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24670	24670	SRR25491989	SRX21223192	SRS18479995	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE cut replicate S10	GSM7676116		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE cut replicate S10	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676116	GSM7676116: KBTRE cut replicate S10; Danio rerio; RNA Seq	GSM7676116 r1	GSM7676116	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	H27K5BCX2_KBTREcut_S10_L002_I1_001.fastq.gz H27K5BCX2_KBTREcut_S10_L002_R1_001.fastq.gz H27K5BCX2_KBTREcut_S10_L002_R2_001.fastq.gz	fastq fastq fastq	1052457252.0	7973161.0	GSM7676116 r5	0:8 1:26 2:98	A:227727118;C:160159228;G:175278732;T:218004542;N:200158	8	26	98	227727118	160159228	175278732	218004542	200158	SRX21223192	SRS18479995	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.91307		0.11551		0.85634		0.50392		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24671	24671	SRR25491990	SRX21223192	SRS18479995	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE cut replicate S10	GSM7676116		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE cut replicate S10	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676116	GSM7676116: KBTRE cut replicate S10; Danio rerio; RNA Seq	GSM7676116 r1	GSM7676116	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HFJ5GBCX2_KBTREcut_S10_L002_I1_001.fastq.gz HFJ5GBCX2_KBTREcut_S10_L002_R1_001.fastq.gz HFJ5GBCX2_KBTREcut_S10_L002_R2_001.fastq.gz	fastq fastq fastq	1003744500.0	7604125.0	GSM7676116 r6	0:8 1:26 2:98	A:217741909;C:152712224;G:167110758;T:207073522;N:565837	8	26	98	217741909	152712224	167110758	207073522	565837	SRX21223192	SRS18479995	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.91357		0.11506		0.85504		0.49763		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24672	24672	SRR25491973	SRX21223191	SRS18479994	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE cut replicate S11	GSM7676117		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE cut replicate S11	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676117	GSM7676117: KBTRE cut replicate S11; Danio rerio; RNA Seq	GSM7676117 r1	GSM7676117	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	H27K5BCX2_KBTREcut_S11_L001_I1_001.fastq.gz H27K5BCX2_KBTREcut_S11_L001_R1_001.fastq.gz H27K5BCX2_KBTREcut_S11_L001_R2_001.fastq.gz	fastq fastq fastq	927688740.0	7027945.0	GSM7676117 r1	0:8 1:26 2:98	A:200105466;C:141029173;G:154321296;T:193068023;N:214652	8	26	98	200105466	141029173	154321296	193068023	214652	SRX21223191	SRS18479994	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.91282		0.1155		0.85283		0.5061		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24673	24673	SRR25491974	SRX21223191	SRS18479994	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE cut replicate S11	GSM7676117		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE cut replicate S11	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676117	GSM7676117: KBTRE cut replicate S11; Danio rerio; RNA Seq	GSM7676117 r1	GSM7676117	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HFJ5GBCX2_KBTREcut_S11_L001_R2_001.fastq.gz HFJ5GBCX2_KBTREcut_S11_L001_R1_001.fastq.gz HFJ5GBCX2_KBTREcut_S11_L001_I1_001.fastq.gz	fastq fastq fastq	897789420.0	6801435.0	GSM7676117 r2	0:8 1:26 2:98	A:193853631;C:136435624;G:149320255;T:186400739;N:530381	8	26	98	193853631	136435624	149320255	186400739	530381	SRX21223191	SRS18479994	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.91186		0.11485		0.85429		0.49592		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24674	24674	SRR25491975	SRX21223191	SRS18479994	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE cut replicate S11	GSM7676117		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE cut replicate S11	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676117	GSM7676117: KBTRE cut replicate S11; Danio rerio; RNA Seq	GSM7676117 r1	GSM7676117	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYLGMBCXY_KBTREcut_S11_L001_R2_001.fastq.gz HYLGMBCXY_KBTREcut_S11_L001_R1_001.fastq.gz HYLGMBCXY_KBTREcut_S11_L001_I1_001.fastq.gz	fastq fastq fastq	978294372.0	7411321.0	GSM7676117 r3	0:8 1:26 2:98	A:211132117;C:148425540;G:162317813;T:201164320;N:3269668	8	26	98	211132117	148425540	162317813	201164320	3269668	SRX21223191	SRS18479994	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.91073		0.1132		0.8537		0.50609		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24675	24675	SRR25491976	SRX21223191	SRS18479994	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE cut replicate S11	GSM7676117		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE cut replicate S11	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676117	GSM7676117: KBTRE cut replicate S11; Danio rerio; RNA Seq	GSM7676117 r1	GSM7676117	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYWGVBCXY_KBTREcut_S11_L001_I1_001.fastq.gz HYWGVBCXY_KBTREcut_S11_L001_R1_001.fastq.gz HYWGVBCXY_KBTREcut_S11_L001_R2_001.fastq.gz	fastq fastq fastq	918264996.0	6956553.0	GSM7676117 r4	0:8 1:26 2:98	A:198352554;C:139394187;G:152576773;T:191275437;N:143243	8	26	98	198352554	139394187	152576773	191275437	143243	SRX21223191	SRS18479994	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.91014		0.1139		0.85307		0.50536		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24676	24676	SRR25491977	SRX21223191	SRS18479994	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE cut replicate S11	GSM7676117		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE cut replicate S11	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676117	GSM7676117: KBTRE cut replicate S11; Danio rerio; RNA Seq	GSM7676117 r1	GSM7676117	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	H27K5BCX2_KBTREcut_S11_L002_I1_001.fastq.gz H27K5BCX2_KBTREcut_S11_L002_R1_001.fastq.gz H27K5BCX2_KBTREcut_S11_L002_R2_001.fastq.gz	fastq fastq fastq	918134580.0	6955565.0	GSM7676117 r5	0:8 1:26 2:98	A:198094257;C:139568875;G:152735838;T:191072590;N:173810	8	26	98	198094257	139568875	152735838	191072590	173810	SRX21223191	SRS18479994	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.91196		0.11403		0.85267		0.50361		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24677	24677	SRR25491978	SRX21223191	SRS18479994	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE cut replicate S11	GSM7676117		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE cut replicate S11	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676117	GSM7676117: KBTRE cut replicate S11; Danio rerio; RNA Seq	GSM7676117 r1	GSM7676117	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HFJ5GBCX2_KBTREcut_S11_L002_I1_001.fastq.gz HFJ5GBCX2_KBTREcut_S11_L002_R1_001.fastq.gz HFJ5GBCX2_KBTREcut_S11_L002_R2_001.fastq.gz	fastq fastq fastq	868525152.0	6579736.0	GSM7676117 r6	0:8 1:26 2:98	A:187572958;C:132014722;G:144495273;T:180237409;N:493766	8	26	98	187572958	132014722	144495273	180237409	493766	SRX21223191	SRS18479994	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.91049		0.11265		0.85273		0.49392		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24678	24678	SRR25491979	SRX21223191	SRS18479994	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE cut replicate S11	GSM7676117		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE cut replicate S11	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676117	GSM7676117: KBTRE cut replicate S11; Danio rerio; RNA Seq	GSM7676117 r1	GSM7676117	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYLGMBCXY_KBTREcut_S11_L002_I1_001.fastq.gz HYLGMBCXY_KBTREcut_S11_L002_R1_001.fastq.gz HYLGMBCXY_KBTREcut_S11_L002_R2_001.fastq.gz	fastq fastq fastq	967222872.0	7327446.0	GSM7676117 r7	0:8 1:26 2:98	A:208757589;C:146699883;G:160504752;T:198933585;N:3193899	8	26	98	208757589	146699883	160504752	198933585	3193899	SRX21223191	SRS18479994	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.91068		0.11108		0.85449		0.48271		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24679	24679	SRR25491980	SRX21223191	SRS18479994	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE cut replicate S11	GSM7676117		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE cut replicate S11	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676117	GSM7676117: KBTRE cut replicate S11; Danio rerio; RNA Seq	GSM7676117 r1	GSM7676117	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYWGVBCXY_KBTREcut_S11_L002_I1_001.fastq.gz HYWGVBCXY_KBTREcut_S11_L002_R1_001.fastq.gz HYWGVBCXY_KBTREcut_S11_L002_R2_001.fastq.gz	fastq fastq fastq	918366636.0	6957323.0	GSM7676117 r8	0:8 1:26 2:98	A:198420992;C:139446089;G:152636322;T:191270874;N:43377	8	26	98	198420992	139446089	152636322	191270874	43377	SRX21223191	SRS18479994	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.91125		0.11279		0.85212		0.49708		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24680	24680	SRR25491981	SRX21223190	SRS18479993	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S8	GSM7676115		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S8	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676115	GSM7676115: KBTGR normal replicate S8; Danio rerio; RNA Seq	GSM7676115 r1	GSM7676115	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	H27K5BCX2_KBTGRnormal_S8_L001_I1_001.fastq.gz H27K5BCX2_KBTGRnormal_S8_L001_R1_001.fastq.gz H27K5BCX2_KBTGRnormal_S8_L001_R2_001.fastq.gz	fastq fastq fastq	1367764332.0	10361851.0	GSM7676115 r1	0:8 1:26 2:98	A:291792120;C:211871917;G:233940380;T:277543215;N:313766	8	26	98	291792120	211871917	233940380	277543215	313766	SRX21223190	SRS18479993	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92841		0.09159		0.82191		0.48306		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24681	24681	SRR25491982	SRX21223190	SRS18479993	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S8	GSM7676115		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S8	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676115	GSM7676115: KBTGR normal replicate S8; Danio rerio; RNA Seq	GSM7676115 r1	GSM7676115	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HFJ5GBCX2_KBTGRnormal_S8_L001_I1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S8_L001_R1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S8_L001_R2_001.fastq.gz	fastq fastq fastq	1324750284.0	10035987.0	GSM7676115 r2	0:8 1:26 2:98	A:282670428;C:205193043;G:226649784;T:268220709;N:792762	8	26	98	282670428	205193043	226649784	268220709	792762	SRX21223190	SRS18479993	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92859		0.09205		0.82039		0.48039		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24682	24682	SRR25491983	SRX21223190	SRS18479993	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S8	GSM7676115		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S8	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676115	GSM7676115: KBTGR normal replicate S8; Danio rerio; RNA Seq	GSM7676115 r1	GSM7676115	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYLGMBCXY_KBTGRnormal_S8_L001_I1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S8_L001_R1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S8_L001_R2_001.fastq.gz	fastq fastq fastq	1442154120.0	10925410.0	GSM7676115 r3	0:8 1:26 2:98	A:307172615;C:223150292;G:246311885;T:289234193;N:4821195	8	26	98	307172615	223150292	246311885	289234193	4821195	SRX21223190	SRS18479993	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92841		0.08941		0.82331		0.49215		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24683	24683	SRR25491984	SRX21223190	SRS18479993	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S8	GSM7676115		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S8	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676115	GSM7676115: KBTGR normal replicate S8; Danio rerio; RNA Seq	GSM7676115 r1	GSM7676115	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYWGVBCXY_KBTGRnormal_S8_L001_I1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S8_L001_R1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S8_L001_R2_001.fastq.gz	fastq fastq fastq	1358634684.0	10292687.0	GSM7676115 r4	0:8 1:26 2:98	A:290016958;C:210290529;G:232317191;T:275847772;N:210876	8	26	98	290016958	210290529	232317191	275847772	210876	SRX21223190	SRS18479993	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92745		0.09192		0.82229		0.49666		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24684	24684	SRR25491985	SRX21223190	SRS18479993	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S8	GSM7676115		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S8	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676115	GSM7676115: KBTGR normal replicate S8; Danio rerio; RNA Seq	GSM7676115 r1	GSM7676115	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	H27K5BCX2_KBTGRnormal_S8_L002_I1_001.fastq.gz H27K5BCX2_KBTGRnormal_S8_L002_R1_001.fastq.gz H27K5BCX2_KBTGRnormal_S8_L002_R2_001.fastq.gz	fastq fastq fastq	1353664092.0	10255031.0	GSM7676115 r5	0:8 1:26 2:98	A:288847376;C:209739068;G:231593033;T:274552362;N:261199	8	26	98	288847376	209739068	231593033	274552362	261199	SRX21223190	SRS18479993	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92838		0.09211		0.82207		0.48301		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24685	24685	SRR25491986	SRX21223190	SRS18479993	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S8	GSM7676115		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S8	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676115	GSM7676115: KBTGR normal replicate S8; Danio rerio; RNA Seq	GSM7676115 r1	GSM7676115	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HFJ5GBCX2_KBTGRnormal_S8_L002_I1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S8_L002_R1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S8_L002_R2_001.fastq.gz	fastq fastq fastq	1282964496.0	9719428.0	GSM7676115 r6	0:8 1:26 2:98	A:273803342;C:198769671;G:219587842;T:259615174;N:727915	8	26	98	273803342	198769671	219587842	259615174	727915	SRX21223190	SRS18479993	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92815		0.09094		0.82189		0.47933		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24686	24686	SRR25491987	SRX21223190	SRS18479993	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S8	GSM7676115		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S8	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676115	GSM7676115: KBTGR normal replicate S8; Danio rerio; RNA Seq	GSM7676115 r1	GSM7676115	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYLGMBCXY_KBTGRnormal_S8_L002_I1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S8_L002_R1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S8_L002_R2_001.fastq.gz	fastq fastq fastq	1425314880.0	10797840.0	GSM7676115 r7	0:8 1:26 2:98	A:303654013;C:220453444;G:243409971;T:285937241;N:4733651	8	26	98	303654013	220453444	243409971	285937241	4733651	SRX21223190	SRS18479993	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92724		0.09059		0.82345		0.49626		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24687	24687	SRR25491988	SRX21223190	SRS18479993	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S8	GSM7676115		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S8	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676115	GSM7676115: KBTGR normal replicate S8; Danio rerio; RNA Seq	GSM7676115 r1	GSM7676115	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYWGVBCXY_KBTGRnormal_S8_L002_I1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S8_L002_R1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S8_L002_R2_001.fastq.gz	fastq fastq fastq	1358584788.0	10292309.0	GSM7676115 r8	0:8 1:26 2:98	A:290131069;C:210271668;G:232237599;T:275940105;N:65841	8	26	98	290131069	210271668	232237599	275940105	65841	SRX21223190	SRS18479993	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92858		0.09144		0.82089		0.49057		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24688	24688	SRR25491991	SRX21223189	SRS18479992	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S7	GSM7676114		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S7	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676114	GSM7676114: KBTGR normal replicate S7; Danio rerio; RNA Seq	GSM7676114 r1	GSM7676114	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	H27K5BCX2_KBTGRnormal_S7_L001_I1_001.fastq.gz H27K5BCX2_KBTGRnormal_S7_L001_R1_001.fastq.gz H27K5BCX2_KBTGRnormal_S7_L001_R2_001.fastq.gz	fastq fastq fastq	1045774224.0	7922532.0	GSM7676114 r1	0:8 1:26 2:98	A:224743708;C:161896286;G:178467180;T:211061243;N:239719	8	26	98	224743708	161896286	178467180	211061243	239719	SRX21223189	SRS18479992	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92898		0.0948		0.82576		0.48767		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24689	24689	SRR25491992	SRX21223189	SRS18479992	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S7	GSM7676114		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S7	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676114	GSM7676114: KBTGR normal replicate S7; Danio rerio; RNA Seq	GSM7676114 r1	GSM7676114	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HFJ5GBCX2_KBTGRnormal_S7_L001_I1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S7_L001_R1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S7_L001_R2_001.fastq.gz	fastq fastq fastq	1023737880.0	7755590.0	GSM7676114 r2	0:8 1:26 2:98	A:220339751;C:158506697;G:174717320;T:205879340;N:604712	8	26	98	220339751	158506697	174717320	205879340	604712	SRX21223189	SRS18479992	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.93138		0.09445		0.82319		0.49095		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24690	24690	SRR25491993	SRX21223189	SRS18479992	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S7	GSM7676114		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S7	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676114	GSM7676114: KBTGR normal replicate S7; Danio rerio; RNA Seq	GSM7676114 r1	GSM7676114	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYLGMBCXY_KBTGRnormal_S7_L001_I1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S7_L001_R1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S7_L001_R2_001.fastq.gz	fastq fastq fastq	1107722484.0	8391837.0	GSM7676114 r3	0:8 1:26 2:98	A:237628383;C:171310823;G:188847113;T:220892571;N:3721136	8	26	98	237628383	171310823	188847113	220892571	3721136	SRX21223189	SRS18479992	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92932		0.09165		0.82432		0.48843		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24691	24691	SRR25491994	SRX21223189	SRS18479992	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S7	GSM7676114		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S7	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676114	GSM7676114: KBTGR normal replicate S7; Danio rerio; RNA Seq	GSM7676114 r1	GSM7676114	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYWGVBCXY_KBTGRnormal_S7_L001_I1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S7_L001_R1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S7_L001_R2_001.fastq.gz	fastq fastq fastq	1018155600.0	7713300.0	GSM7676114 r4	0:8 1:26 2:98	A:218785960;C:157467573;G:173782025;T:205710180;N:157662	8	26	98	218785960	157467573	173782025	205710180	157662	SRX21223189	SRS18479992	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92735		0.09294		0.82304		0.48936		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24692	24692	SRR25491995	SRX21223189	SRS18479992	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S7	GSM7676114		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S7	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676114	GSM7676114: KBTGR normal replicate S7; Danio rerio; RNA Seq	GSM7676114 r1	GSM7676114	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	H27K5BCX2_KBTGRnormal_S7_L002_I1_001.fastq.gz H27K5BCX2_KBTGRnormal_S7_L002_R1_001.fastq.gz H27K5BCX2_KBTGRnormal_S7_L002_R2_001.fastq.gz	fastq fastq fastq	1037896992.0	7862856.0	GSM7676114 r5	0:8 1:26 2:98	A:222624793;C:160770752;G:177337819;T:209629234;N:197290	8	26	98	222624793	160770752	177337819	209629234	197290	SRX21223189	SRS18479992	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.93038		0.09291		0.82513		0.48834		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24693	24693	SRR25491996	SRX21223189	SRS18479992	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S7	GSM7676114		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S7	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676114	GSM7676114: KBTGR normal replicate S7; Danio rerio; RNA Seq	GSM7676114 r1	GSM7676114	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HFJ5GBCX2_KBTGRnormal_S7_L002_I1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S7_L002_R1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S7_L002_R2_001.fastq.gz	fastq fastq fastq	994648116.0	7535213.0	GSM7676114 r6	0:8 1:26 2:98	A:213918528;C:154046950;G:169913173;T:200006956;N:565267	8	26	98	213918528	154046950	169913173	200006956	565267	SRX21223189	SRS18479992	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92863		0.09237		0.8244		0.48574		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24694	24694	SRR25491997	SRX21223189	SRS18479992	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S7	GSM7676114		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S7	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676114	GSM7676114: KBTGR normal replicate S7; Danio rerio; RNA Seq	GSM7676114 r1	GSM7676114	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYLGMBCXY_KBTGRnormal_S7_L002_I1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S7_L002_R1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S7_L002_R2_001.fastq.gz	fastq fastq fastq	1095910068.0	8302349.0	GSM7676114 r7	0:8 1:26 2:98	A:235361030;C:169424678;G:186752468;T:218466797;N:3625229	8	26	98	235361030	169424678	186752468	218466797	3625229	SRX21223189	SRS18479992	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92887		0.09019		0.82696		0.4934		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24695	24695	SRR25491998	SRX21223189	SRS18479992	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S7	GSM7676114		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S7	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676114	GSM7676114: KBTGR normal replicate S7; Danio rerio; RNA Seq	GSM7676114 r1	GSM7676114	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYWGVBCXY_KBTGRnormal_S7_L002_I1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S7_L002_R1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S7_L002_R2_001.fastq.gz	fastq fastq fastq	1020164640.0	7728520.0	GSM7676114 r8	0:8 1:26 2:98	A:219455597;C:157669416;G:174033845;T:206187545;N:48557	8	26	98	219455597	157669416	174033845	206187545	48557	SRX21223189	SRS18479992	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.93		0.0929		0.82507		0.48822		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24696	24696	SRR25491999	SRX21223188	SRS18479991	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S6	GSM7676113		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S6	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676113	GSM7676113: KBTGR normal replicate S6; Danio rerio; RNA Seq	GSM7676113 r1	GSM7676113	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	H27K5BCX2_KBTGRnormal_S6_L001_I1_001.fastq.gz H27K5BCX2_KBTGRnormal_S6_L001_R1_001.fastq.gz H27K5BCX2_KBTGRnormal_S6_L001_R2_001.fastq.gz	fastq fastq fastq	1289409660.0	9768255.0	GSM7676113 r1	0:8 1:26 2:98	A:275297633;C:199461255;G:220403674;T:261830960;N:295468	8	26	98	275297633	199461255	220403674	261830960	295468	SRX21223188	SRS18479991	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92761		0.09178		0.82089		0.49952		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24697	24697	SRR25492000	SRX21223188	SRS18479991	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S6	GSM7676113		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S6	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676113	GSM7676113: KBTGR normal replicate S6; Danio rerio; RNA Seq	GSM7676113 r1	GSM7676113	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HFJ5GBCX2_KBTGRnormal_S6_L001_I1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S6_L001_R1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S6_L001_R2_001.fastq.gz	fastq fastq fastq	1254104148.0	9500789.0	GSM7676113 r2	0:8 1:26 2:98	A:267759276;C:194047461;G:214469796;T:254057804;N:742985	8	26	98	267759276	194047461	214469796	254057804	742985	SRX21223188	SRS18479991	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92863		0.09263		0.82016		0.49849		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24698	24698	SRR25492001	SRX21223188	SRS18479991	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S6	GSM7676113		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S6	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676113	GSM7676113: KBTGR normal replicate S6; Danio rerio; RNA Seq	GSM7676113 r1	GSM7676113	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYLGMBCXY_KBTGRnormal_S6_L001_I1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S6_L001_R1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S6_L001_R2_001.fastq.gz	fastq fastq fastq	1364037444.0	10333617.0	GSM7676113 r3	0:8 1:26 2:98	A:290782963;C:210764004;G:232828321;T:273741440;N:4577738	8	26	98	290782963	210764004	232828321	273741440	4577738	SRX21223188	SRS18479991	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92727		0.09037		0.82339		0.49743		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24699	24699	SRR25492002	SRX21223188	SRS18479991	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S6	GSM7676113		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S6	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676113	GSM7676113: KBTGR normal replicate S6; Danio rerio; RNA Seq	GSM7676113 r1	GSM7676113	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYWGVBCXY_KBTGRnormal_S6_L001_I1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S6_L001_R1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S6_L001_R2_001.fastq.gz	fastq fastq fastq	1274535900.0	9655575.0	GSM7676113 r4	0:8 1:26 2:98	A:272331035;C:196919570;G:217674747;T:259126322;N:194676	8	26	98	272331035	196919570	217674747	259126322	194676	SRX21223188	SRS18479991	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.9267		0.09131		0.82193		0.49736		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24700	24700	SRR25492003	SRX21223188	SRS18479991	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S6	GSM7676113		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S6	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676113	GSM7676113: KBTGR normal replicate S6; Danio rerio; RNA Seq	GSM7676113 r1	GSM7676113	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	H27K5BCX2_KBTGRnormal_S6_L002_I1_001.fastq.gz H27K5BCX2_KBTGRnormal_S6_L002_R1_001.fastq.gz H27K5BCX2_KBTGRnormal_S6_L002_R2_001.fastq.gz	fastq fastq fastq	1278788544.0	9687792.0	GSM7676113 r5	0:8 1:26 2:98	A:273089526;C:197794682;G:218629305;T:259640660;N:249443	8	26	98	273089526	197794682	218629305	259640660	249443	SRX21223188	SRS18479991	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92837		0.09211		0.82069		0.49043		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24701	24701	SRR25492004	SRX21223188	SRS18479991	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S6	GSM7676113		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S6	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676113	GSM7676113: KBTGR normal replicate S6; Danio rerio; RNA Seq	GSM7676113 r1	GSM7676113	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HFJ5GBCX2_KBTGRnormal_S6_L002_I1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S6_L002_R1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S6_L002_R2_001.fastq.gz	fastq fastq fastq	1218538200.0	9231350.0	GSM7676113 r6	0:8 1:26 2:98	A:260174350;C:188588952;G:208442781;T:246771528;N:694689	8	26	98	260174350	188588952	208442781	246771528	694689	SRX21223188	SRS18479991	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92755		0.09174		0.82152		0.48524		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24702	24702	SRR25492005	SRX21223188	SRS18479991	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S6	GSM7676113		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S6	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676113	GSM7676113: KBTGR normal replicate S6; Danio rerio; RNA Seq	GSM7676113 r1	GSM7676113	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYLGMBCXY_KBTGRnormal_S6_L002_I1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S6_L002_R1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S6_L002_R2_001.fastq.gz	fastq fastq fastq	1348885428.0	10218829.0	GSM7676113 r7	0:8 1:26 2:98	A:287599265;C:208361077;G:230218011;T:270815023;N:4451866	8	26	98	287599265	208361077	230218011	270815023	4451866	SRX21223188	SRS18479991	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92616		0.08938		0.82189		0.49517		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24703	24703	SRR25492006	SRX21223188	SRS18479991	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S6	GSM7676113		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S6	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676113	GSM7676113: KBTGR normal replicate S6; Danio rerio; RNA Seq	GSM7676113 r1	GSM7676113	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYWGVBCXY_KBTGRnormal_S6_L002_I1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S6_L002_R1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S6_L002_R2_001.fastq.gz	fastq fastq fastq	1274044596.0	9651853.0	GSM7676113 r8	0:8 1:26 2:98	A:272274110;C:196868273;G:217614843;T:259062639;N:61729	8	26	98	272274110	196868273	217614843	259062639	61729	SRX21223188	SRS18479991	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92673		0.09105		0.82142		0.48867		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24704	24704	SRR25492007	SRX21223187	SRS18479990	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S5	GSM7676112		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S5	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676112	GSM7676112: KBTGR normal replicate S5; Danio rerio; RNA Seq	GSM7676112 r1	GSM7676112	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	H27K5BCX2_KBTGRnormal_S5_L001_I1_001.fastq.gz H27K5BCX2_KBTGRnormal_S5_L001_R1_001.fastq.gz H27K5BCX2_KBTGRnormal_S5_L001_R2_001.fastq.gz	fastq fastq fastq	1258754244.0	9536017.0	GSM7676112 r1	0:8 1:26 2:98	A:269418553;C:194370105;G:214652075;T:255806804;N:282129	8	26	98	269418553	194370105	214652075	255806804	282129	SRX21223187	SRS18479990	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.9286		0.09296		0.82288		0.48038		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24705	24705	SRR25492008	SRX21223187	SRS18479990	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S5	GSM7676112		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S5	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676112	GSM7676112: KBTGR normal replicate S5; Danio rerio; RNA Seq	GSM7676112 r1	GSM7676112	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HFJ5GBCX2_KBTGRnormal_S5_L001_I1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S5_L001_R1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S5_L001_R2_001.fastq.gz	fastq fastq fastq	1217159724.0	9220907.0	GSM7676112 r2	0:8 1:26 2:98	A:260789467;C:187945962;G:207550436;T:246642449;N:720572	8	26	98	260789467	187945962	207550436	246642449	720572	SRX21223187	SRS18479990	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.93045		0.09356		0.82386		0.4736		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24706	24706	SRR25492009	SRX21223187	SRS18479990	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S5	GSM7676112		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S5	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676112	GSM7676112: KBTGR normal replicate S5; Danio rerio; RNA Seq	GSM7676112 r1	GSM7676112	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYLGMBCXY_KBTGRnormal_S5_L001_I1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S5_L001_R1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S5_L001_R2_001.fastq.gz	fastq fastq fastq	1327996824.0	10060582.0	GSM7676112 r3	0:8 1:26 2:98	A:283722392;C:204894097;G:226054109;T:266823827;N:4442611	8	26	98	283722392	204894097	226054109	266823827	4442611	SRX21223187	SRS18479990	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92793		0.09118		0.82513		0.48007		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24707	24707	SRR25492010	SRX21223187	SRS18479990	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S5	GSM7676112		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S5	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676112	GSM7676112: KBTGR normal replicate S5; Danio rerio; RNA Seq	GSM7676112 r1	GSM7676112	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYWGVBCXY_KBTGRnormal_S5_L001_I1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S5_L001_R1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S5_L001_R2_001.fastq.gz	fastq fastq fastq	1255655808.0	9512544.0	GSM7676112 r4	0:8 1:26 2:98	A:268848025;C:193752306;G:214061624;T:255371933;N:195424	8	26	98	268848025	193752306	214061624	255371933	195424	SRX21223187	SRS18479990	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92719		0.09327		0.82221		0.47626		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24708	24708	SRR25492011	SRX21223187	SRS18479990	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S5	GSM7676112		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S5	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676112	GSM7676112: KBTGR normal replicate S5; Danio rerio; RNA Seq	GSM7676112 r1	GSM7676112	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	H27K5BCX2_KBTGRnormal_S5_L002_I1_001.fastq.gz H27K5BCX2_KBTGRnormal_S5_L002_R1_001.fastq.gz H27K5BCX2_KBTGRnormal_S5_L002_R2_001.fastq.gz	fastq fastq fastq	1246449072.0	9442796.0	GSM7676112 r5	0:8 1:26 2:98	A:266772235;C:192514744;G:212592908;T:253285733;N:228388	8	26	98	266772235	192514744	212592908	253285733	228388	SRX21223187	SRS18479990	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92776		0.09295		0.82333		0.48441		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24709	24709	SRR25492012	SRX21223187	SRS18479990	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S5	GSM7676112		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S5	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676112	GSM7676112: KBTGR normal replicate S5; Danio rerio; RNA Seq	GSM7676112 r1	GSM7676112	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HFJ5GBCX2_KBTGRnormal_S5_L002_I1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S5_L002_R1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S5_L002_R2_001.fastq.gz	fastq fastq fastq	1176943812.0	8916241.0	GSM7676112 r6	0:8 1:26 2:98	A:252114687;C:181782204;G:200782194;T:238444957;N:667576	8	26	98	252114687	181782204	200782194	238444957	667576	SRX21223187	SRS18479990	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92798		0.09407		0.82225		0.47898		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24710	24710	SRR25492013	SRX21223187	SRS18479990	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S5	GSM7676112		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S5	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676112	GSM7676112: KBTGR normal replicate S5; Danio rerio; RNA Seq	GSM7676112 r1	GSM7676112	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYLGMBCXY_KBTGRnormal_S5_L002_I1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S5_L002_R1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S5_L002_R2_001.fastq.gz	fastq fastq fastq	1312162368.0	9940624.0	GSM7676112 r7	0:8 1:26 2:98	A:280415120;C:202362829;G:223408996;T:263680714;N:4313493	8	26	98	280415120	202362829	223408996	263680714	4313493	SRX21223187	SRS18479990	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.9269		0.09153		0.82386		0.48775		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24711	24711	SRR25492014	SRX21223187	SRS18479990	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR normal replicate S5	GSM7676112		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR normal replicate S5	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676112	GSM7676112: KBTGR normal replicate S5; Danio rerio; RNA Seq	GSM7676112 r1	GSM7676112	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYWGVBCXY_KBTGRnormal_S5_L002_I1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S5_L002_R1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S5_L002_R2_001.fastq.gz	fastq fastq fastq	1254798732.0	9506051.0	GSM7676112 r8	0:8 1:26 2:98	A:268758608;C:193670297;G:213835768;T:255268464;N:59861	8	26	98	268758608	193670297	213835768	255268464	59861	SRX21223187	SRS18479990	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.9283		0.09341		0.82211		0.49121		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24712	24712	SRR25492015	SRX21223186	SRS18479989	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR cut replicate S16	GSM7676111		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR cut replicate S16	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676111	GSM7676111: KBTGR cut replicate S16; Danio rerio; RNA Seq	GSM7676111 r1	GSM7676111	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	H27K5BCX2_KBTGRcut_S16_L001_I1_001.fastq.gz H27K5BCX2_KBTGRcut_S16_L001_R1_001.fastq.gz H27K5BCX2_KBTGRcut_S16_L001_R2_001.fastq.gz	fastq fastq fastq	1733777364.0	13134677.0	GSM7676111 r1	0:8 1:26 2:98	A:377310857;C:268033707;G:292815269;T:348639631;N:398882	8	26	98	377310857	268033707	292815269	348639631	398882	SRX21223186	SRS18479989	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92457		0.10972		0.83684		0.49054		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24713	24713	SRR25492016	SRX21223186	SRS18479989	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR cut replicate S16	GSM7676111		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR cut replicate S16	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676111	GSM7676111: KBTGR cut replicate S16; Danio rerio; RNA Seq	GSM7676111 r1	GSM7676111	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HFJ5GBCX2_KBTGRcut_S16_L001_I1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S16_L001_R1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S16_L001_R2_001.fastq.gz	fastq fastq fastq	1693931844.0	12832817.0	GSM7676111 r2	0:8 1:26 2:98	A:370335488;C:261641086;G:285793090;T:338853348;N:993054	8	26	98	370335488	261641086	285793090	338853348	993054	SRX21223186	SRS18479989	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.9257		0.11044		0.83593		0.49929		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24714	24714	SRR25492017	SRX21223186	SRS18479989	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR cut replicate S16	GSM7676111		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR cut replicate S16	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676111	GSM7676111: KBTGR cut replicate S16; Danio rerio; RNA Seq	GSM7676111 r1	GSM7676111	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYLGMBCXY_KBTGRcut_S16_L001_I1_001.fastq.gz HYLGMBCXY_KBTGRcut_S16_L001_R1_001.fastq.gz HYLGMBCXY_KBTGRcut_S16_L001_R2_001.fastq.gz	fastq fastq fastq	1822627488.0	13807784.0	GSM7676111 r3	0:8 1:26 2:98	A:396109320;C:281479505;G:307344748;T:362166256;N:6063003	8	26	98	396109320	281479505	307344748	362166256	6063003	SRX21223186	SRS18479989	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.9237		0.1075		0.83733		0.49995		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24715	24715	SRR25492018	SRX21223186	SRS18479989	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR cut replicate S16	GSM7676111		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR cut replicate S16	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676111	GSM7676111: KBTGR cut replicate S16; Danio rerio; RNA Seq	GSM7676111 r1	GSM7676111	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYWGVBCXY_KBTGRcut_S16_L001_I1_001.fastq.gz HYWGVBCXY_KBTGRcut_S16_L001_R1_001.fastq.gz HYWGVBCXY_KBTGRcut_S16_L001_R2_001.fastq.gz	fastq fastq fastq	1686941784.0	12779862.0	GSM7676111 r4	0:8 1:26 2:98	A:366995826;C:260455612;G:284984185;T:339737397;N:253456	8	26	98	366995826	260455612	284984185	339737397	253456	SRX21223186	SRS18479989	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92245		0.10934		0.83583		0.5109		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24716	24716	SRR25492019	SRX21223186	SRS18479989	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR cut replicate S16	GSM7676111		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR cut replicate S16	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676111	GSM7676111: KBTGR cut replicate S16; Danio rerio; RNA Seq	GSM7676111 r1	GSM7676111	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYLGMBCXY_KBTGRcut_S16_L002_I1_001.fastq.gz HYLGMBCXY_KBTGRcut_S16_L002_R1_001.fastq.gz HYLGMBCXY_KBTGRcut_S16_L002_R2_001.fastq.gz	fastq fastq fastq	1800605268.0	13640949.0	GSM7676111 r7	0:8 1:26 2:98	A:392033512;C:277884536;G:303332072;T:357657308;N:5905574	8	26	98	392033512	277884536	303332072	357657308	5905574	SRX21223186	SRS18479989	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92264		0.10865		0.83771		0.4962		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24717	24717	SRR25492020	SRX21223186	SRS18479989	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR cut replicate S16	GSM7676111		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR cut replicate S16	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676111	GSM7676111: KBTGR cut replicate S16; Danio rerio; RNA Seq	GSM7676111 r1	GSM7676111	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYWGVBCXY_KBTGRcut_S16_L002_I1_001.fastq.gz HYWGVBCXY_KBTGRcut_S16_L002_R1_001.fastq.gz HYWGVBCXY_KBTGRcut_S16_L002_R2_001.fastq.gz	fastq fastq fastq	1687212120.0	12781910.0	GSM7676111 r8	0:8 1:26 2:98	A:367591713;C:260374660;G:284790982;T:339790038;N:79787	8	26	98	367591713	260374660	284790982	339790038	79787	SRX21223186	SRS18479989	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92439		0.11008		0.83252		0.48566		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24718	24718	SRR25492035	SRX21223186	SRS18479989	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR cut replicate S16	GSM7676111		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR cut replicate S16	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676111	GSM7676111: KBTGR cut replicate S16; Danio rerio; RNA Seq	GSM7676111 r1	GSM7676111	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	H27K5BCX2_KBTGRcut_S16_L002_I1_001.fastq.gz H27K5BCX2_KBTGRcut_S16_L002_R1_001.fastq.gz H27K5BCX2_KBTGRcut_S16_L002_R2_001.fastq.gz	fastq fastq fastq	1715599116.0	12996963.0	GSM7676111 r5	0:8 1:26 2:98	A:372113041;C:265506989;G:290255809;T:345508071;N:318464	8	26	98	372113041	265506989	290255809	345508071	318464	SRX21223186	SRS18479989	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92368		0.10681		0.83727		0.49306		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24719	24719	SRR25492036	SRX21223186	SRS18479989	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR cut replicate S16	GSM7676111		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR cut replicate S16	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676111	GSM7676111: KBTGR cut replicate S16; Danio rerio; RNA Seq	GSM7676111 r1	GSM7676111	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HFJ5GBCX2_KBTGRcut_S16_L002_I1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S16_L002_R1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S16_L002_R2_001.fastq.gz	fastq fastq fastq	1643667564.0	12452027.0	GSM7676111 r6	0:8 1:26 2:98	A:358646057;C:254091415;G:277620310;T:329013074;N:927790	8	26	98	358646057	254091415	277620310	329013074	927790	SRX21223186	SRS18479989	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92527		0.1079		0.83465		0.49184		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24720	24720	SRR25492021	SRX21223185	SRS18479988	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE normal replicate S2	GSM7676121		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE normal replicate S2	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676121	GSM7676121: KBTRE normal replicate S2; Danio rerio; RNA Seq	GSM7676121 r1	GSM7676121	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	H27K5BCX2_KBTREnormal_S2_L001_I1_001.fastq.gz H27K5BCX2_KBTREnormal_S2_L001_R1_001.fastq.gz H27K5BCX2_KBTREnormal_S2_L001_R2_001.fastq.gz	fastq fastq fastq	807188844.0	6115067.0	GSM7676121 r1	0:8 1:26 2:98	A:172308620;C:125913345;G:139442237;T:161426336;N:186028	8	26	98	172308620	125913345	139442237	161426336	186028	SRX21223185	SRS18479988	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92298		0.08811		0.85433		0.4736		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24721	24721	SRR25492022	SRX21223185	SRS18479988	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE normal replicate S2	GSM7676121		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE normal replicate S2	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676121	GSM7676121: KBTRE normal replicate S2; Danio rerio; RNA Seq	GSM7676121 r1	GSM7676121	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HFJ5GBCX2_KBTREnormal_S2_L001_I1_001.fastq.gz HFJ5GBCX2_KBTREnormal_S2_L001_R1_001.fastq.gz HFJ5GBCX2_KBTREnormal_S2_L001_R2_001.fastq.gz	fastq fastq fastq	793147344.0	6008692.0	GSM7676121 r2	0:8 1:26 2:98	A:169497439;C:123759266;G:137078289;T:158052236;N:464586	8	26	98	169497439	123759266	137078289	158052236	464586	SRX21223185	SRS18479988	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92361		0.08644		0.85464		0.47495		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24722	24722	SRR25492023	SRX21223185	SRS18479988	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE normal replicate S2	GSM7676121		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE normal replicate S2	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676121	GSM7676121: KBTRE normal replicate S2; Danio rerio; RNA Seq	GSM7676121 r1	GSM7676121	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYLGMBCXY_KBTREnormal_S2_L001_I1_001.fastq.gz HYLGMBCXY_KBTREnormal_S2_L001_R1_001.fastq.gz HYLGMBCXY_KBTREnormal_S2_L001_R2_001.fastq.gz	fastq fastq fastq	852294828.0	6456779.0	GSM7676121 r3	0:8 1:26 2:98	A:181361509;C:132917413;G:147157966;T:168488477;N:2838977	8	26	98	181361509	132917413	147157966	168488477	2838977	SRX21223185	SRS18479988	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.9234		0.08441		0.85681		0.45235		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24723	24723	SRR25492024	SRX21223185	SRS18479988	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE normal replicate S2	GSM7676121		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE normal replicate S2	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676121	GSM7676121: KBTRE normal replicate S2; Danio rerio; RNA Seq	GSM7676121 r1	GSM7676121	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYWGVBCXY_KBTREnormal_S2_L001_I1_001.fastq.gz HYWGVBCXY_KBTREnormal_S2_L001_R1_001.fastq.gz HYWGVBCXY_KBTREnormal_S2_L001_R2_001.fastq.gz	fastq fastq fastq	781758516.0	5922413.0	GSM7676121 r4	0:8 1:26 2:98	A:166724753;C:121839518;G:135085811;T:156626231;N:120161	8	26	98	166724753	121839518	135085811	156626231	120161	SRX21223185	SRS18479988	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92293		0.08698		0.85626		0.47803		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24724	24724	SRR25492025	SRX21223185	SRS18479988	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE normal replicate S2	GSM7676121		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE normal replicate S2	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676121	GSM7676121: KBTRE normal replicate S2; Danio rerio; RNA Seq	GSM7676121 r1	GSM7676121	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYLGMBCXY_KBTREnormal_S2_L002_I1_001.fastq.gz HYLGMBCXY_KBTREnormal_S2_L002_R1_001.fastq.gz HYLGMBCXY_KBTREnormal_S2_L002_R2_001.fastq.gz	fastq fastq fastq	843137856.0	6387408.0	GSM7676121 r7	0:8 1:26 2:98	A:179558862;C:131385546;G:145540868;T:166696387;N:2784321	8	26	98	179558862	131385546	145540868	166696387	2784321	SRX21223185	SRS18479988	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92281		0.08446		0.85685		0.47524		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24725	24725	SRR25492026	SRX21223185	SRS18479988	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE normal replicate S2	GSM7676121		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE normal replicate S2	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676121	GSM7676121: KBTRE normal replicate S2; Danio rerio; RNA Seq	GSM7676121 r1	GSM7676121	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYWGVBCXY_KBTREnormal_S2_L002_I1_001.fastq.gz HYWGVBCXY_KBTREnormal_S2_L002_R1_001.fastq.gz HYWGVBCXY_KBTREnormal_S2_L002_R2_001.fastq.gz	fastq fastq fastq	782789964.0	5930227.0	GSM7676121 r8	0:8 1:26 2:98	A:167092677;C:121959994;G:135189997;T:156882004;N:37574	8	26	98	167092677	121959994	135189997	156882004	37574	SRX21223185	SRS18479988	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92384		0.08593		0.85529		0.47658		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24726	24726	SRR25492073	SRX21223185	SRS18479988	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE normal replicate S2	GSM7676121		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE normal replicate S2	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676121	GSM7676121: KBTRE normal replicate S2; Danio rerio; RNA Seq	GSM7676121 r1	GSM7676121	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	H27K5BCX2_KBTREnormal_S2_L002_I1_001.fastq.gz H27K5BCX2_KBTREnormal_S2_L002_R1_001.fastq.gz H27K5BCX2_KBTREnormal_S2_L002_R2_001.fastq.gz	fastq fastq fastq	799492452.0	6056761.0	GSM7676121 r5	0:8 1:26 2:98	A:170481537;C:124727025;G:138222223;T:159980825;N:150968	8	26	98	170481537	124727025	138222223	159980825	150968	SRX21223185	SRS18479988	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92219		0.08693		0.85689		0.45239		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24727	24727	SRR25492074	SRX21223185	SRS18479988	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTRE normal replicate S2	GSM7676121		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTRE normal replicate S2	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676121	GSM7676121: KBTRE normal replicate S2; Danio rerio; RNA Seq	GSM7676121 r1	GSM7676121	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HFJ5GBCX2_KBTREnormal_S2_L002_I1_001.fastq.gz HFJ5GBCX2_KBTREnormal_S2_L002_R1_001.fastq.gz HFJ5GBCX2_KBTREnormal_S2_L002_R2_001.fastq.gz	fastq fastq fastq	771619332.0	5845601.0	GSM7676121 r6	0:8 1:26 2:98	A:164827141;C:120458327;G:133444180;T:153706468;N:432782	8	26	98	164827141	120458327	133444180	153706468	432782	SRX21223185	SRS18479988	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.9244		0.086		0.85752		0.46487		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24728	24728	SRR25492027	SRX21223184	SRS18479986	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR cut replicate S15	GSM7676110		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR cut replicate S15	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676110	GSM7676110: KBTGR cut replicate S15; Danio rerio; RNA Seq	GSM7676110 r1	GSM7676110	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	H27K5BCX2_KBTGRcut_S15_L001_I1_001.fastq.gz H27K5BCX2_KBTGRcut_S15_L001_R1_001.fastq.gz H27K5BCX2_KBTGRcut_S15_L001_R2_001.fastq.gz	fastq fastq fastq	991634028.0	7512379.0	GSM7676110 r1	0:8 1:26 2:98	A:213910719;C:153374311;G:167803904;T:200905324;N:218884	8	26	98	213910719	153374311	167803904	200905324	218884	SRX21223184	SRS18479986	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92289		0.10915		0.83163		0.51061		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24729	24729	SRR25492028	SRX21223184	SRS18479986	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR cut replicate S15	GSM7676110		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR cut replicate S15	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676110	GSM7676110: KBTGR cut replicate S15; Danio rerio; RNA Seq	GSM7676110 r1	GSM7676110	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HFJ5GBCX2_KBTGRcut_S15_L001_I1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S15_L001_R1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S15_L001_R2_001.fastq.gz	fastq fastq fastq	973359420.0	7373935.0	GSM7676110 r2	0:8 1:26 2:98	A:210076453;C:150636615;G:164768683;T:196577221;N:586658	8	26	98	210076453	150636615	164768683	196577221	586658	SRX21223184	SRS18479986	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92307		0.10829		0.8309		0.50664		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24730	24730	SRR25492029	SRX21223184	SRS18479986	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR cut replicate S15	GSM7676110		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR cut replicate S15	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676110	GSM7676110: KBTGR cut replicate S15; Danio rerio; RNA Seq	GSM7676110 r1	GSM7676110	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYLGMBCXY_KBTGRcut_S15_L001_I1_001.fastq.gz HYLGMBCXY_KBTGRcut_S15_L001_R1_001.fastq.gz HYLGMBCXY_KBTGRcut_S15_L001_R2_001.fastq.gz	fastq fastq fastq	1041506532.0	7890201.0	GSM7676110 r3	0:8 1:26 2:98	A:224331472;C:160956885;G:176036393;T:208465176;N:3449772	8	26	98	224331472	160956885	176036393	208465176	3449772	SRX21223184	SRS18479986	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92046		0.10509		0.83179		0.5158		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24731	24731	SRR25492030	SRX21223184	SRS18479986	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR cut replicate S15	GSM7676110		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR cut replicate S15	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676110	GSM7676110: KBTGR cut replicate S15; Danio rerio; RNA Seq	GSM7676110 r1	GSM7676110	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYWGVBCXY_KBTGRcut_S15_L001_I1_001.fastq.gz HYWGVBCXY_KBTGRcut_S15_L001_R1_001.fastq.gz HYWGVBCXY_KBTGRcut_S15_L001_R2_001.fastq.gz	fastq fastq fastq	959532816.0	7269188.0	GSM7676110 r4	0:8 1:26 2:98	A:207101192;C:148189510;G:162346748;T:194597135;N:145839	8	26	98	207101192	148189510	162346748	194597135	145839	SRX21223184	SRS18479986	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92159		0.10724		0.83031		0.51032		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24732	24732	SRR25492031	SRX21223184	SRS18479986	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR cut replicate S15	GSM7676110		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR cut replicate S15	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676110	GSM7676110: KBTGR cut replicate S15; Danio rerio; RNA Seq	GSM7676110 r1	GSM7676110	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	H27K5BCX2_KBTGRcut_S15_L002_I1_001.fastq.gz H27K5BCX2_KBTGRcut_S15_L002_R1_001.fastq.gz H27K5BCX2_KBTGRcut_S15_L002_R2_001.fastq.gz	fastq fastq fastq	981662748.0	7436839.0	GSM7676110 r5	0:8 1:26 2:98	A:211518289;C:151920644;G:166249815;T:198931555;N:189919	8	26	98	211518289	151920644	166249815	198931555	189919	SRX21223184	SRS18479986	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92149		0.10822		0.83078		0.51544		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24733	24733	SRR25492032	SRX21223184	SRS18479986	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR cut replicate S15	GSM7676110		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR cut replicate S15	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676110	GSM7676110: KBTGR cut replicate S15; Danio rerio; RNA Seq	GSM7676110 r1	GSM7676110	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HFJ5GBCX2_KBTGRcut_S15_L002_I1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S15_L002_R1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S15_L002_R2_001.fastq.gz	fastq fastq fastq	945758088.0	7164834.0	GSM7676110 r6	0:8 1:26 2:98	A:203967307;C:146422295;G:160254376;T:190978208;N:531546	8	26	98	203967307	146422295	160254376	190978208	531546	SRX21223184	SRS18479986	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92245		0.10759		0.83142		0.51632		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24734	24734	SRR25492033	SRX21223184	SRS18479986	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR cut replicate S15	GSM7676110		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR cut replicate S15	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676110	GSM7676110: KBTGR cut replicate S15; Danio rerio; RNA Seq	GSM7676110 r1	GSM7676110	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYLGMBCXY_KBTGRcut_S15_L002_I1_001.fastq.gz HYLGMBCXY_KBTGRcut_S15_L002_R1_001.fastq.gz HYLGMBCXY_KBTGRcut_S15_L002_R2_001.fastq.gz	fastq fastq fastq	1029633660.0	7800255.0	GSM7676110 r7	0:8 1:26 2:98	A:221920698;C:159045837;G:173908417;T:206140930;N:3409108	8	26	98	221920698	159045837	173908417	206140930	3409108	SRX21223184	SRS18479986	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92088		0.10596		0.83295		0.51602		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24735	24735	SRR25492034	SRX21223184	SRS18479986	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR cut replicate S15	GSM7676110		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR cut replicate S15	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676110	GSM7676110: KBTGR cut replicate S15; Danio rerio; RNA Seq	GSM7676110 r1	GSM7676110	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYWGVBCXY_KBTGRcut_S15_L002_I1_001.fastq.gz HYWGVBCXY_KBTGRcut_S15_L002_R1_001.fastq.gz HYWGVBCXY_KBTGRcut_S15_L002_R2_001.fastq.gz	fastq fastq fastq	960845292.0	7279131.0	GSM7676110 r8	0:8 1:26 2:98	A:207492886;C:148360000;G:162496060;T:194960451;N:45441	8	26	98	207492886	148360000	162496060	194960451	45441	SRX21223184	SRS18479986	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92106		0.10819		0.82946		0.51364		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24736	24736	SRR25492037	SRX21223183	SRS18479987	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR cut replicate S14	GSM7676109		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR cut replicate S14	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676109	GSM7676109: KBTGR cut replicate S14; Danio rerio; RNA Seq	GSM7676109 r1	GSM7676109	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	H27K5BCX2_KBTGRcut_S14_L001_I1_001.fastq.gz H27K5BCX2_KBTGRcut_S14_L001_R1_001.fastq.gz H27K5BCX2_KBTGRcut_S14_L001_R2_001.fastq.gz	fastq fastq fastq	2591037900.0	19629075.0	GSM7676109 r1	0:8 1:26 2:98	A:555580990;C:402990210;G:441965039;T:522520043;N:593068	8	26	98	555580990	402990210	441965039	522520043	593068	SRX21223183	SRS18479987	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92241		0.10605		0.83187		0.51181		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24737	24737	SRR25492038	SRX21223183	SRS18479987	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR cut replicate S14	GSM7676109		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR cut replicate S14	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676109	GSM7676109: KBTGR cut replicate S14; Danio rerio; RNA Seq	GSM7676109 r1	GSM7676109	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HFJ5GBCX2_KBTGRcut_S14_L001_I1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S14_L001_R1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S14_L001_R2_001.fastq.gz	fastq fastq fastq	2497809996.0	18922803.0	GSM7676109 r2	0:8 1:26 2:98	A:535857014;C:388641161;G:426148721;T:502295548;N:1492250	8	26	98	535857014	388641161	426148721	502295548	1492250	SRX21223183	SRS18479987	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92376		0.10611		0.83177		0.49598		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24738	24738	SRR25492039	SRX21223183	SRS18479987	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR cut replicate S14	GSM7676109		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR cut replicate S14	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676109	GSM7676109: KBTGR cut replicate S14; Danio rerio; RNA Seq	GSM7676109 r1	GSM7676109	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYLGMBCXY_KBTGRcut_S14_L001_I1_001.fastq.gz HYLGMBCXY_KBTGRcut_S14_L001_R1_001.fastq.gz HYLGMBCXY_KBTGRcut_S14_L001_R2_001.fastq.gz	fastq fastq fastq	2728654500.0	20671625.0	GSM7676109 r3	0:8 1:26 2:98	A:584168882;C:423983386;G:464567203;T:543992364;N:9107415	8	26	98	584168882	423983386	464567203	543992364	9107415	SRX21223183	SRS18479987	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92388		0.10372		0.83181		0.50245		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24739	24739	SRR25492040	SRX21223183	SRS18479987	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR cut replicate S14	GSM7676109		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR cut replicate S14	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676109	GSM7676109: KBTGR cut replicate S14; Danio rerio; RNA Seq	GSM7676109 r1	GSM7676109	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYWGVBCXY_KBTGRcut_S14_L001_I1_001.fastq.gz HYWGVBCXY_KBTGRcut_S14_L001_R1_001.fastq.gz HYWGVBCXY_KBTGRcut_S14_L001_R2_001.fastq.gz	fastq fastq fastq	2618092488.0	19834034.0	GSM7676109 r4	0:8 1:26 2:98	A:561803683;C:406792207;G:446399294;T:528347486;N:392662	8	26	98	561803683	406792207	446399294	528347486	392662	SRX21223183	SRS18479987	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92126		0.10547		0.83161		0.49641		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24740	24740	SRR25492041	SRX21223183	SRS18479987	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR cut replicate S14	GSM7676109		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR cut replicate S14	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676109	GSM7676109: KBTGR cut replicate S14; Danio rerio; RNA Seq	GSM7676109 r1	GSM7676109	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	H27K5BCX2_KBTGRcut_S14_L002_I1_001.fastq.gz H27K5BCX2_KBTGRcut_S14_L002_R1_001.fastq.gz H27K5BCX2_KBTGRcut_S14_L002_R2_001.fastq.gz	fastq fastq fastq	2564163096.0	19425478.0	GSM7676109 r5	0:8 1:26 2:98	A:549889204;C:398857562;G:437417974;T:517052381;N:479723	8	26	98	549889204	398857562	437417974	517052381	479723	SRX21223183	SRS18479987	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.9232		0.1061		0.83071		0.50282		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24741	24741	SRR25492042	SRX21223183	SRS18479987	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR cut replicate S14	GSM7676109		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR cut replicate S14	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676109	GSM7676109: KBTGR cut replicate S14; Danio rerio; RNA Seq	GSM7676109 r1	GSM7676109	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HFJ5GBCX2_KBTGRcut_S14_L002_I1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S14_L002_R1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S14_L002_R2_001.fastq.gz	fastq fastq fastq	2415052992.0	18295856.0	GSM7676109 r6	0:8 1:26 2:98	A:517947164;C:375865420;G:412233894;T:485594270;N:1353140	8	26	98	517947164	375865420	412233894	485594270	1353140	SRX21223183	SRS18479987	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92288		0.10488		0.82899		0.4957		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24742	24742	SRR25492043	SRX21223183	SRS18479987	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR cut replicate S14	GSM7676109		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR cut replicate S14	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676109	GSM7676109: KBTGR cut replicate S14; Danio rerio; RNA Seq	GSM7676109 r1	GSM7676109	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYLGMBCXY_KBTGRcut_S14_L002_I1_001.fastq.gz HYLGMBCXY_KBTGRcut_S14_L002_R1_001.fastq.gz HYLGMBCXY_KBTGRcut_S14_L002_R2_001.fastq.gz	fastq fastq fastq	2694434160.0	20412380.0	GSM7676109 r7	0:8 1:26 2:98	A:576891044;C:418621857;G:458706495;T:537348616;N:8845228	8	26	98	576891044	418621857	458706495	537348616	8845228	SRX21223183	SRS18479987	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.9222		0.10385		0.83114		0.50871		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures
24743	24743	SRR25492044	SRX21223183	SRS18479987	SRP452960	PRJNA1001330	Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish	GSE239880	Transcriptome Analysis	The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins and which exert non overlapping functions. However there is little information about ontogenetically distinct neutrophil populations. In this work using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2 we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly caudal neutrophils respond heterogeneously. Collectively our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times at 34hpf and 44hpf and performed caudal fin transections at 54hpf on the half of each group. Three hours later we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.			KBTGR cut replicate S14	GSM7676109		source name:whole embryo\|tissue:whole embryo\|cell type:neutrophils\|geo loc name:missing\|collection date:missing	KBTGR cut replicate S14	Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files	whole embryo	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	tissue:whole embryo\|cell type:neutrophils	GSM7676109	GSM7676109: KBTGR cut replicate S14; Danio rerio; RNA Seq	GSM7676109 r1	GSM7676109	1	For tissue disaggregation whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription GEMs were broken and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing 2 adapter ligation 3 postligation cleanup with SPRIselect 4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP452960		loader:fastq load.py	HYWGVBCXY_KBTGRcut_S14_L002_I1_001.fastq.gz HYWGVBCXY_KBTGRcut_S14_L002_R1_001.fastq.gz HYWGVBCXY_KBTGRcut_S14_L002_R2_001.fastq.gz	fastq fastq fastq	2615928216.0	19817638.0	GSM7676109 r8	0:8 1:26 2:98	A:561516458;C:406357695;G:445851758;T:528279876;N:122737	8	26	98	561516458	406357695	445851758	528279876	122737	SRX21223183	SRS18479987	SRA1685258	Facultad de Ciencias de la vida, Universidad Andres Bello	Facultad de Ciencias de la vida, Universidad Andres Bello	1	0.92228		0.10465		0.8297		0.49948		98		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	Chile	2023-08-02	Undetermined	Embryo	Whole Organism	All anatomical structures

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