metadata: run_metadata: 1,401 rows where experiment.library_layout = "PAIRED", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and tissue

1,401 rows where experiment.library_layout = "PAIRED", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and tissue_curation = "Whole Organism"

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.attributes	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.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
11130	11130	ERR9979395	ERX9520370	ERS12499848	ERP139765	PRJEB54901	Single cell RNA sequencing of germ free zebrafish embryos	E-MTAB-11984	Transcriptome Analysis	The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish. Here we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.	ENA FIRST PUBLIC:2022 07 22\|ENA LAST UPDATE:2022 07 22	Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate four replicates i.e. eighty larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM w…	Sample 2 WT GO+BA	SAMEA110401656	Institute of Environmental Medicine, Karolinska Institutet	ENA FIRST PUBLIC:2022 07 22\|ENA LAST UPDATE:2022 07 22\|External Id:SAMEA110401656\|INSDC center alias:Institute of Environmental Medicine Karolinska Institutet\|INSDC center name:Institute of Environmental Medicine Karolinska Institutet\|INSDC first public:2022 07 22T16:26:50Z\|INSDC last update:2022 07 22T16:26:50Z\|INSDC status:public\|Submitter Id:E MTAB 11984:Sample 2 WT GO+BA\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|genotype:wild type genotype\|individual:pool of 80 individuals\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 11984:Sample 2 WT GO+BA\|sex:not available\|stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM\|strain:AB							Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos	E MTAB 11984:Sample 2 WT GO+BA p	Sample 2 WT GO+BA p	Single cell RNA sequencing of germ free zebrafish embryos	The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate four replicates i.e. eighty larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM with 10% FBS…	Experimental Factor: stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM	AMPLICON	TRANSCRIPTOMIC SINGLE CELL	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP139765	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos	ENA FIRST PUBLIC:2022 07 22\|ENA LAST UPDATE:2022 07 22	P22202_7002_S2_L002_R1_001.fastq.gz P22202_7002_S2_L002_R2_001.fastq.gz	fastq fastq	18144406998.0	153766161.0	E MTAB 11984:P22202 7002 S2 L002	0:28 1:90	A:5277424121;C:3880928155;G:4118706097;T:4866649878;N:698747	28	90			5277424121	3880928155	4118706097	4866649878	698747	ERX9520370	ERS12499848	ERA16483151	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	2	0.0109	0.90145	0.0053	0.21373	0.98746	0.79423	0.41198	0.54447	28	90	T	B	sc-like readlen	illumina	novaseq_era	full_length	size_fractionation	trueseq	sc	single_cell_droplet	10x	Sweden	2022-07-22	Multi-stage	Embryo	Whole Organism	All anatomical structures
11131	11131	ERR9979394	ERX9520370	ERS12499848	ERP139765	PRJEB54901	Single cell RNA sequencing of germ free zebrafish embryos	E-MTAB-11984	Transcriptome Analysis	The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish. Here we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.	ENA FIRST PUBLIC:2022 07 22\|ENA LAST UPDATE:2022 07 22	Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate four replicates i.e. eighty larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM w…	Sample 2 WT GO+BA	SAMEA110401656	Institute of Environmental Medicine, Karolinska Institutet	ENA FIRST PUBLIC:2022 07 22\|ENA LAST UPDATE:2022 07 22\|External Id:SAMEA110401656\|INSDC center alias:Institute of Environmental Medicine Karolinska Institutet\|INSDC center name:Institute of Environmental Medicine Karolinska Institutet\|INSDC first public:2022 07 22T16:26:50Z\|INSDC last update:2022 07 22T16:26:50Z\|INSDC status:public\|Submitter Id:E MTAB 11984:Sample 2 WT GO+BA\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|genotype:wild type genotype\|individual:pool of 80 individuals\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 11984:Sample 2 WT GO+BA\|sex:not available\|stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM\|strain:AB							Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos	E MTAB 11984:Sample 2 WT GO+BA p	Sample 2 WT GO+BA p	Single cell RNA sequencing of germ free zebrafish embryos	The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate four replicates i.e. eighty larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM with 10% FBS…	Experimental Factor: stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM	AMPLICON	TRANSCRIPTOMIC SINGLE CELL	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP139765	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos	ENA FIRST PUBLIC:2022 07 22\|ENA LAST UPDATE:2022 07 22	P22202_7002_S2_L001_R1_001.fastq.gz P22202_7002_S2_L001_R2_001.fastq.gz	fastq fastq	18458951574.0	156431793.0	E MTAB 11984:P22202 7002 S2 L001	0:28 1:90	A:5372920926;C:3946687814;G:4185647697;T:4953205454;N:489683	28	90			5372920926	3946687814	4185647697	4953205454	489683	ERX9520370	ERS12499848	ERA16483151	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	2	0.01037	0.90168	0.0048	0.21246	0.98752	0.79297	0.42601	0.54996	28	90	T	B	sc-like readlen	illumina	novaseq_era	full_length	size_fractionation	trueseq	sc	single_cell_droplet	10x	Sweden	2022-07-22	Multi-stage	Embryo	Whole Organism	All anatomical structures
11132	11132	ERR9979392	ERX9520369	ERS12499847	ERP139765	PRJEB54901	Single cell RNA sequencing of germ free zebrafish embryos	E-MTAB-11984	Transcriptome Analysis	The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish. Here we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.	ENA FIRST PUBLIC:2022 07 22\|ENA LAST UPDATE:2022 07 22	Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate four replicates i.e. eighty larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM w…	Sample 1 WT control	SAMEA110401655	Institute of Environmental Medicine, Karolinska Institutet	ENA FIRST PUBLIC:2022 07 22\|ENA LAST UPDATE:2022 07 22\|External Id:SAMEA110401655\|INSDC center alias:Institute of Environmental Medicine Karolinska Institutet\|INSDC center name:Institute of Environmental Medicine Karolinska Institutet\|INSDC first public:2022 07 22T16:26:50Z\|INSDC last update:2022 07 22T16:26:50Z\|INSDC status:public\|Submitter Id:E MTAB 11984:Sample 1 WT control\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|genotype:wild type genotype\|individual:pool of 80 individuals\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 11984:Sample 1 WT control\|sex:not available\|stimulus:n1\|strain:AB							Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos	E MTAB 11984:Sample 1 WT control p	Sample 1 WT control p	Single cell RNA sequencing of germ free zebrafish embryos	The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate four replicates i.e. eighty larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM with 10% FBS…	Experimental Factor: stimulus:n1	AMPLICON	TRANSCRIPTOMIC SINGLE CELL	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP139765	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos	ENA FIRST PUBLIC:2022 07 22\|ENA LAST UPDATE:2022 07 22	P22202_7001_S1_L001_R1_001.fastq.gz P22202_7001_S1_L001_R2_001.fastq.gz	fastq fastq	19396994226.0	164381307.0	E MTAB 11984:P22202 7001 S1 L001	0:28 1:90	A:5665199484;C:4091196594;G:4415211076;T:5224866754;N:520318	28	90			5665199484	4091196594	4415211076	5224866754	520318	ERX9520369	ERS12499847	ERA16483151	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	2	0.01093	0.89238	0.00557	0.232	0.98764	0.79444	0.40806	0.54781	28	90	T	B	sc-like readlen	illumina	novaseq_era	full_length	size_fractionation	trueseq	sc	single_cell_droplet	10x	Sweden	2022-07-22	Multi-stage	Embryo	Whole Organism	All anatomical structures
11133	11133	ERR9979393	ERX9520369	ERS12499847	ERP139765	PRJEB54901	Single cell RNA sequencing of germ free zebrafish embryos	E-MTAB-11984	Transcriptome Analysis	The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish. Here we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.	ENA FIRST PUBLIC:2022 07 22\|ENA LAST UPDATE:2022 07 22	Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate four replicates i.e. eighty larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM w…	Sample 1 WT control	SAMEA110401655	Institute of Environmental Medicine, Karolinska Institutet	ENA FIRST PUBLIC:2022 07 22\|ENA LAST UPDATE:2022 07 22\|External Id:SAMEA110401655\|INSDC center alias:Institute of Environmental Medicine Karolinska Institutet\|INSDC center name:Institute of Environmental Medicine Karolinska Institutet\|INSDC first public:2022 07 22T16:26:50Z\|INSDC last update:2022 07 22T16:26:50Z\|INSDC status:public\|Submitter Id:E MTAB 11984:Sample 1 WT control\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|genotype:wild type genotype\|individual:pool of 80 individuals\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 11984:Sample 1 WT control\|sex:not available\|stimulus:n1\|strain:AB							Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos	E MTAB 11984:Sample 1 WT control p	Sample 1 WT control p	Single cell RNA sequencing of germ free zebrafish embryos	The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate four replicates i.e. eighty larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM with 10% FBS…	Experimental Factor: stimulus:n1	AMPLICON	TRANSCRIPTOMIC SINGLE CELL	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP139765	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos	ENA FIRST PUBLIC:2022 07 22\|ENA LAST UPDATE:2022 07 22	P22202_7001_S1_L002_R1_001.fastq.gz P22202_7001_S1_L002_R2_001.fastq.gz	fastq fastq	19063958224.0	161558968.0	E MTAB 11984:P22202 7001 S1 L002	0:28 1:90	A:5563588848;C:4022930643;G:4344549562;T:5132136743;N:752428	28	90			5563588848	4022930643	4344549562	5132136743	752428	ERX9520369	ERS12499847	ERA16483151	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	2	0.01118	0.89308	0.00573	0.23128	0.98737	0.79354	0.39264	0.54552	28	90	T	B	sc-like readlen	illumina	novaseq_era	full_length	size_fractionation	trueseq	sc	single_cell_droplet	10x	Sweden	2022-07-22	Multi-stage	Embryo	Whole Organism	All anatomical structures
11134	11134	ERR9981089	ERX9522049	ERS12503451	ERP139797	PRJEB54930	Single cell RNA sequencing of lck GFP transgenic zebrafish	E-MTAB-11991	Transcriptome Analysis	The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23	Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate four replicates i.e. two hundred larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing u…	Sample 1 lck control	SAMEA110406305	Institute of Environmental Medicine, Karolinska Institutet	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23\|External Id:SAMEA110406305\|INSDC center alias:Institute of Environmental Medicine Karolinska Institutet\|INSDC center name:Institute of Environmental Medicine Karolinska Institutet\|INSDC first public:2022 07 23T04:33:35Z\|INSDC last update:2022 07 23T04:33:35Z\|INSDC status:public\|Submitter Id:E MTAB 11991:Sample 1 lck control\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larva\|disease:normal\|genotype:wild type genotype\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 11991:Sample 1 lck control\|strain:Tglck:GFP							Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish	E MTAB 11991:Sample 1 lck control p	Sample 1 lck control p	Single cell RNA sequencing of lck GFP transgenic zebrafish	The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate four replicates i.e. two hundred larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM w…	Experimental Factor: stimulus:n1	AMPLICON	TRANSCRIPTOMIC SINGLE CELL	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP139797	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23	P25452_2002_S2_L001_R1_001.fastq.gz P25452_2002_S2_L001_R2_001.fastq.gz	fastq fastq	60177283876.0	509976982.0	E MTAB 11991:P25452 2002 S2 L001	0:28 1:90	A:17254566438;C:13547211711;G:14188233429;T:15185192817;N:2079481	28	90			17254566438	13547211711	14188233429	15185192817	2079481	ERX9522049	ERS12503451	ERA16488297	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	2	0.00671	0.93031	0.00231	0.11028	0.9932	0.82227	0.30887	0.58272	28	90	T	B	sc-like readlen	illumina	novaseq_era	full_length	size_fractionation	trueseq	sc	single_cell_droplet	10x	Sweden	2022-07-23	Larval	Larval	Whole Organism	All anatomical structures
11135	11135	ERR9981090	ERX9522049	ERS12503451	ERP139797	PRJEB54930	Single cell RNA sequencing of lck GFP transgenic zebrafish	E-MTAB-11991	Transcriptome Analysis	The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23	Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate four replicates i.e. two hundred larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing u…	Sample 1 lck control	SAMEA110406305	Institute of Environmental Medicine, Karolinska Institutet	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23\|External Id:SAMEA110406305\|INSDC center alias:Institute of Environmental Medicine Karolinska Institutet\|INSDC center name:Institute of Environmental Medicine Karolinska Institutet\|INSDC first public:2022 07 23T04:33:35Z\|INSDC last update:2022 07 23T04:33:35Z\|INSDC status:public\|Submitter Id:E MTAB 11991:Sample 1 lck control\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larva\|disease:normal\|genotype:wild type genotype\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 11991:Sample 1 lck control\|strain:Tglck:GFP							Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish	E MTAB 11991:Sample 1 lck control p	Sample 1 lck control p	Single cell RNA sequencing of lck GFP transgenic zebrafish	The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate four replicates i.e. two hundred larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM w…	Experimental Factor: stimulus:n1	AMPLICON	TRANSCRIPTOMIC SINGLE CELL	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP139797	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23	P25452_2002_S2_L002_R1_001.fastq.gz P25452_2002_S2_L002_R2_001.fastq.gz	fastq fastq	60597886144.0	513541408.0	E MTAB 11991:P25452 2002 S2 L002	0:28 1:90	A:17368154358;C:13649089056;G:14296037620;T:15282869484;N:1735626	28	90			17368154358	13649089056	14296037620	15282869484	1735626	ERX9522049	ERS12503451	ERA16488297	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	2	0.00656	0.92899	0.00211	0.11059	0.99334	0.82335	0.32311	0.57644	28	90	T	B	sc-like readlen	illumina	novaseq_era	full_length	size_fractionation	trueseq	sc	single_cell_droplet	10x	Sweden	2022-07-23	Larval	Larval	Whole Organism	All anatomical structures
11136	11136	ERR9981087	ERX9522048	ERS12503450	ERP139797	PRJEB54930	Single cell RNA sequencing of lck GFP transgenic zebrafish	E-MTAB-11991	Transcriptome Analysis	The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23	Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate four replicates i.e. two hundred larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing u…	Sample 2 lck GO+BA	SAMEA110406304	Institute of Environmental Medicine, Karolinska Institutet	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23\|External Id:SAMEA110406304\|INSDC center alias:Institute of Environmental Medicine Karolinska Institutet\|INSDC center name:Institute of Environmental Medicine Karolinska Institutet\|INSDC first public:2022 07 23T04:33:35Z\|INSDC last update:2022 07 23T04:33:35Z\|INSDC status:public\|Submitter Id:E MTAB 11991:Sample 2 lck GO+BA\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larva\|disease:normal\|genotype:wild type genotype\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 11991:Sample 2 lck GO+BA\|strain:Tglck:GFP							Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish	E MTAB 11991:Sample 2 lck GO+BA p	Sample 2 lck GO+BA p	Single cell RNA sequencing of lck GFP transgenic zebrafish	The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate four replicates i.e. two hundred larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM w…	Experimental Factor: stimulus:graphene oxide 30 microgram per milliliter\|Experimental Factor: compound:butyrate\|Experimental Factor: dose:2.5	AMPLICON	TRANSCRIPTOMIC SINGLE CELL	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP139797	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23	P25452_2001_S1_L001_R1_001.fastq.gz P25452_2001_S1_L001_R2_001.fastq.gz	fastq fastq	20866120186.0	176831527.0	E MTAB 11991:P25452 2001 S1 L001	0:28 1:90	A:5933525376;C:4737179804;G:5025711080;T:5168983880;N:720046	28	90			5933525376	4737179804	5025711080	5168983880	720046	ERX9522048	ERS12503450	ERA16488297	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	2	0.00805	0.92622	0.00259	0.11842	0.99302	0.83027	0.2729	0.57699	28	90	T	B	sc-like readlen	illumina	novaseq_era	full_length	size_fractionation	trueseq	sc	single_cell_droplet	10x	Sweden	2022-07-23	Larval	Larval	Whole Organism	All anatomical structures
11137	11137	ERR9981088	ERX9522048	ERS12503450	ERP139797	PRJEB54930	Single cell RNA sequencing of lck GFP transgenic zebrafish	E-MTAB-11991	Transcriptome Analysis	The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23	Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate four replicates i.e. two hundred larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing u…	Sample 2 lck GO+BA	SAMEA110406304	Institute of Environmental Medicine, Karolinska Institutet	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23\|External Id:SAMEA110406304\|INSDC center alias:Institute of Environmental Medicine Karolinska Institutet\|INSDC center name:Institute of Environmental Medicine Karolinska Institutet\|INSDC first public:2022 07 23T04:33:35Z\|INSDC last update:2022 07 23T04:33:35Z\|INSDC status:public\|Submitter Id:E MTAB 11991:Sample 2 lck GO+BA\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larva\|disease:normal\|genotype:wild type genotype\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 11991:Sample 2 lck GO+BA\|strain:Tglck:GFP							Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish	E MTAB 11991:Sample 2 lck GO+BA p	Sample 2 lck GO+BA p	Single cell RNA sequencing of lck GFP transgenic zebrafish	The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate four replicates i.e. two hundred larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM w…	Experimental Factor: stimulus:graphene oxide 30 microgram per milliliter\|Experimental Factor: compound:butyrate\|Experimental Factor: dose:2.5	AMPLICON	TRANSCRIPTOMIC SINGLE CELL	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP139797	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23	P25452_2001_S1_L002_R1_001.fastq.gz P25452_2001_S1_L002_R2_001.fastq.gz	fastq fastq	21068682172.0	178548154.0	E MTAB 11991:P25452 2001 S1 L002	0:28 1:90	A:5987758267;C:4786100132;G:5078292970;T:5215926275;N:604528	28	90			5987758267	4786100132	5078292970	5215926275	604528	ERX9522048	ERS12503450	ERA16488297	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	2	0.00813	0.92702	0.00264	0.11874	0.99283	0.82737	0.30228	0.56929	28	90	T	B	sc-like readlen	illumina	novaseq_era	full_length	size_fractionation	trueseq	sc	single_cell_droplet	10x	Sweden	2022-07-23	Larval	Larval	Whole Organism	All anatomical structures
11238	11238	ERR10782555	ERX10233132	ERS14439197	ERP144048	PRJEB58983	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E-MTAB-12503	Transcriptome Analysis	Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our…	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Sample 6	E MTAB 12503:Sample 6		strain:mixed AB and Tubingen\|ENA FIRST PUBLIC:2023 03 31\|individual:20170530.A 6\|organism:Danio rerio\|organism:Danio rerio\|ENA LAST UPDATE:2023 03 31\|scientific name:Danio rerio\|common name:zebrafish\|organism part:embryo\|age:10\|developmental stage:bud\|genotype:wild type genotype\|ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31							Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E MTAB 12503:Sample 6 p	Sample 6 p	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Experimental Factor: developmental stage:bud\|Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	ERP144048	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	20170530.A-6_R1.fastq.gz 20170530.A-6_R2.fastq.gz	fastq fastq	14809693138.0	49038719.0	E MTAB 12503:20170530.A 6 R	0:151 1:151	A:4069749497;C:3367864217;G:3430269434;T:3928390721;N:13419269	151	151			4069749497	3367864217	3430269434	3928390721	13419269	ERX10233132	ERS14439197	ERA20162442	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	2	0.83945	0.69977	0.27269	0.22488	0.74523	0.77654	0.4899	0.4358	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	trueseq	sc	unknown	unknown	Switzerland	2023-03-31	Multi-stage	Embryo	Whole Organism	All anatomical structures
11239	11239	ERR10782554	ERX10233131	ERS14439196	ERP144048	PRJEB58983	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E-MTAB-12503	Transcriptome Analysis	Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our…	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Sample 5	E MTAB 12503:Sample 5		strain:mixed AB and Tubingen\|ENA FIRST PUBLIC:2023 03 31\|individual:20170530.A 5\|organism:Danio rerio\|organism:Danio rerio\|ENA LAST UPDATE:2023 03 31\|scientific name:Danio rerio\|common name:zebrafish\|organism part:embryo\|age:10\|developmental stage:bud\|genotype:wild type genotype\|ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31							Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E MTAB 12503:Sample 5 p	Sample 5 p	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Experimental Factor: developmental stage:bud\|Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	ERP144048	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	20170530.A-5_R1.fastq.gz 20170530.A-5_R2.fastq.gz	fastq fastq	14954968728.0	49519764.0	E MTAB 12503:20170530.A 5 R	0:151 1:151	A:4063340262;C:3440933120;G:3455723079;T:3981396987;N:13575280	151	151			4063340262	3440933120	3455723079	3981396987	13575280	ERX10233131	ERS14439196	ERA20162442	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	2	0.85891	0.86859	0.28842	0.28866	0.7349	0.75051	0.45532	0.49145	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	trueseq	sc	unknown	unknown	Switzerland	2023-03-31	Multi-stage	Embryo	Whole Organism	All anatomical structures
11240	11240	ERR10782553	ERX10233130	ERS14439195	ERP144048	PRJEB58983	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E-MTAB-12503	Transcriptome Analysis	Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our…	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Sample 2	E MTAB 12503:Sample 2		strain:mixed AB and Tubingen\|ENA FIRST PUBLIC:2023 03 31\|individual:20170530.A 2\|organism:Danio rerio\|organism:Danio rerio\|ENA LAST UPDATE:2023 03 31\|scientific name:Danio rerio\|common name:zebrafish\|organism part:embryo\|age:24\|developmental stage:pharyngula prim 5\|genotype:wild type genotype\|ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31							Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E MTAB 12503:Sample 2 p	Sample 2 p	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Experimental Factor: developmental stage:pharyngula prim 5\|Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	ERP144048	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	20170530.A-2_R1.fastq.gz 20170530.A-2_R2.fastq.gz	fastq fastq	16267571562.0	53866131.0	E MTAB 12503:20170530.A 2 R	0:151 1:151	A:4395815325;C:3765428574;G:3780844712;T:4310729283;N:14753668	151	151			4395815325	3765428574	3780844712	4310729283	14753668	ERX10233130	ERS14439195	ERA20162442	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	2	0.86977	0.8727	0.28497	0.28427	0.70763	0.72301	0.47478	0.47986	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	trueseq	sc	unknown	unknown	Switzerland	2023-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
11241	11241	ERR10782552	ERX10233129	ERS14439194	ERP144048	PRJEB58983	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E-MTAB-12503	Transcriptome Analysis	Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our…	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Sample 1	E MTAB 12503:Sample 1		strain:mixed AB and Tubingen\|ENA FIRST PUBLIC:2023 03 31\|individual:20170530.A 1\|organism:Danio rerio\|organism:Danio rerio\|ENA LAST UPDATE:2023 03 31\|scientific name:Danio rerio\|common name:zebrafish\|organism part:embryo\|age:24\|developmental stage:pharyngula prim 5\|genotype:wild type genotype\|ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31							Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E MTAB 12503:Sample 1 p	Sample 1 p	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Experimental Factor: developmental stage:pharyngula prim 5\|Experimental Factor: genotype:wild type genotype	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	ERP144048	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	20170530.A-1_R1.fastq.gz 20170530.A-1_R2.fastq.gz	fastq fastq	15446599662.0	51147681.0	E MTAB 12503:20170530.A 1 R	0:151 1:151	A:4289931639;C:3451135010;G:3474244788;T:4217248893;N:14039332	151	151			4289931639	3451135010	3474244788	4217248893	14039332	ERX10233129	ERS14439194	ERA20162442	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	2	0.90114	0.90507	0.32128	0.32127	0.70232	0.71956	0.47336	0.47528	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	trueseq	sc	unknown	unknown	Switzerland	2023-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
11242	11242	ERR10782551	ERX10233128	ERS14439193	ERP144048	PRJEB58983	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E-MTAB-12503	Transcriptome Analysis	Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our…	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Sample 7	E MTAB 12503:Sample 7		strain:mixed AB and Tubingen\|ENA FIRST PUBLIC:2023 03 31\|individual:20170530.A 7\|organism:Danio rerio\|organism:Danio rerio\|ENA LAST UPDATE:2023 03 31\|scientific name:Danio rerio\|common name:zebrafish\|organism part:embryo\|age:10\|developmental stage:bud\|genotype:rbm8a d5/d5\|ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31							Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E MTAB 12503:Sample 7 p	Sample 7 p	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Experimental Factor: developmental stage:bud\|Experimental Factor: genotype:rbm8a d5/d5	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	ERP144048	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	20170530.A-7_R1.fastq.gz 20170530.A-7_R2.fastq.gz	fastq fastq	12726557236.0	42140918.0	E MTAB 12503:20170530.A 7 R	0:151 1:151	A:3510176970;C:2879679978;G:2932244172;T:3392911734;N:11544382	151	151			3510176970	2879679978	2932244172	3392911734	11544382	ERX10233128	ERS14439193	ERA20162442	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	2	0.88531	0.88678	0.33279	0.3329	0.73545	0.74992	0.52548	0.52864	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	trueseq	sc	unknown	unknown	Switzerland	2023-03-31	Multi-stage	Embryo	Whole Organism	All anatomical structures
11243	11243	ERR10782550	ERX10233127	ERS14439192	ERP144048	PRJEB58983	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E-MTAB-12503	Transcriptome Analysis	Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our…	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Sample 4	E MTAB 12503:Sample 4		strain:mixed AB and Tubingen\|ENA FIRST PUBLIC:2023 03 31\|individual:20170530.A 4\|organism:Danio rerio\|organism:Danio rerio\|ENA LAST UPDATE:2023 03 31\|scientific name:Danio rerio\|common name:zebrafish\|organism part:embryo\|age:24\|developmental stage:pharyngula prim 5\|genotype:rbm8a d5/d5\|ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31							Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E MTAB 12503:Sample 4 p	Sample 4 p	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Experimental Factor: developmental stage:pharyngula prim 5\|Experimental Factor: genotype:rbm8a d5/d5	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	ERP144048	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	20170530.A-4_R1.fastq.gz 20170530.A-4_R2.fastq.gz	fastq fastq	15697575554.0	51978727.0	E MTAB 12503:20170530.A 4 R	0:151 1:151	A:4256444510;C:3622485921;G:3650190489;T:4154211501;N:14243133	151	151			4256444510	3622485921	3650190489	4154211501	14243133	ERX10233127	ERS14439192	ERA20162442	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	2	0.87714	0.88071	0.29319	0.29235	0.69844	0.7164	0.47594	0.47385	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	trueseq	sc	unknown	unknown	Switzerland	2023-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
11244	11244	ERR10782549	ERX10233126	ERS14439191	ERP144048	PRJEB58983	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E-MTAB-12503	Transcriptome Analysis	Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our…	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Sample 3	E MTAB 12503:Sample 3		strain:mixed AB and Tubingen\|ENA FIRST PUBLIC:2023 03 31\|individual:20170530.A 3\|organism:Danio rerio\|organism:Danio rerio\|ENA LAST UPDATE:2023 03 31\|scientific name:Danio rerio\|common name:zebrafish\|organism part:embryo\|age:24\|developmental stage:pharyngula prim 5\|genotype:rbm8a d5/d5\|ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31							Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	E MTAB 12503:Sample 3 p	Sample 3 p	RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturerâ€™s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.	Experimental Factor: developmental stage:pharyngula prim 5\|Experimental Factor: genotype:rbm8a d5/d5	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 4000	ERP144048	Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling	ENA FIRST PUBLIC:2023 03 31\|ENA LAST UPDATE:2023 03 31	20170530.A-3_R1.fastq.gz 20170530.A-3_R2.fastq.gz	fastq fastq	13839085674.0	45824787.0	E MTAB 12503:20170530.A 3 R	0:151 1:151	A:3812423011;C:3120168590;G:3163957945;T:3729983766;N:12552362	151	151			3812423011	3120168590	3163957945	3729983766	12552362	ERX10233126	ERS14439191	ERA20162442	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	2	0.88987	0.74432	0.33651	0.27875	0.69229	0.72934	0.46981	0.46116	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	trueseq	sc	unknown	unknown	Switzerland	2023-03-31	Pharyngula	Embryo	Whole Organism	All anatomical structures
15009	15009	ERR12306826	ERX11683773	ERS17043893	ERP155237	PRJEB70303	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E-MTAB-13554	Transcriptome Analysis	To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule but containing a detection fluorophores. post treatment the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30	Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.	Coated	SAMEA114641726	KIS	ENA first public:2024 09 30\|External Id:SAMEA114641726\|INSDC center name:KIS\|INSDC last update:2023 11 20T16:06:50Z\|INSDC status:public\|Submitter Id:E MTAB 13554:Coated\|age:2\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 13554:Coated\|scientific name:Danio rerio\|sex:not available\|strain:transgenic lines Tgfli1:EGFPy1							10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E MTAB 13554:Coated p	Coated p	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	ILLUMINA	NextSeq 550	ERP155237	NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30	230324-Coated_S1_L003_I1_001.fastq.gz 230324-Coated_S1_L003_I2_001.fastq.gz 230324-Coated_S1_L003_R1_001.fastq.gz 230324-Coated_S1_L003_R2_001.fastq.gz	fastq fastq fastq fastq	10050750400.0	62817190.0	E MTAB 13554:230324 Coated S1 L003	0:10 1:10 2:30 3:110	A:1894211982;C:1556769050;G:1595134885;T:1863244619;N:530364	10	10	30	110	1894211982	1556769050	1595134885	1863244619	530364	ERX11683773	ERS17043893	ERA27417303	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-11-20	Hatching	Embryo	Whole Organism	All anatomical structures
15010	15010	ERR12306829	ERX11683773	ERS17043893	ERP155237	PRJEB70303	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E-MTAB-13554	Transcriptome Analysis	To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule but containing a detection fluorophores. post treatment the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30	Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.	Coated	SAMEA114641726	KIS	ENA first public:2024 09 30\|External Id:SAMEA114641726\|INSDC center name:KIS\|INSDC last update:2023 11 20T16:06:50Z\|INSDC status:public\|Submitter Id:E MTAB 13554:Coated\|age:2\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 13554:Coated\|scientific name:Danio rerio\|sex:not available\|strain:transgenic lines Tgfli1:EGFPy1							10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E MTAB 13554:Coated p	Coated p	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	ILLUMINA	NextSeq 550	ERP155237	NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30	230324-Coated_S1_L004_I1_001.fastq.gz 230324-Coated_S1_L004_I2_001.fastq.gz 230324-Coated_S1_L004_R1_001.fastq.gz 230324-Coated_S1_L004_R2_001.fastq.gz	fastq fastq fastq fastq	9780757760.0	61129736.0	E MTAB 13554:230324 Coated S1 L004	0:10 1:10 2:30 3:110	A:1844808667;C:1516149264;G:1549838165;T:1813091860;N:383004	10	10	30	110	1844808667	1516149264	1549838165	1813091860	383004	ERX11683773	ERS17043893	ERA27417303	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-11-20	Hatching	Embryo	Whole Organism	All anatomical structures
15011	15011	ERR12306828	ERX11683773	ERS17043893	ERP155237	PRJEB70303	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E-MTAB-13554	Transcriptome Analysis	To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule but containing a detection fluorophores. post treatment the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30	Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.	Coated	SAMEA114641726	KIS	ENA first public:2024 09 30\|External Id:SAMEA114641726\|INSDC center name:KIS\|INSDC last update:2023 11 20T16:06:50Z\|INSDC status:public\|Submitter Id:E MTAB 13554:Coated\|age:2\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 13554:Coated\|scientific name:Danio rerio\|sex:not available\|strain:transgenic lines Tgfli1:EGFPy1							10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E MTAB 13554:Coated p	Coated p	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	ILLUMINA	NextSeq 550	ERP155237	NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30	230324-Coated_S1_L002_I1_001.fastq.gz 230324-Coated_S1_L002_I2_001.fastq.gz 230324-Coated_S1_L002_R1_001.fastq.gz 230324-Coated_S1_L002_R2_001.fastq.gz	fastq fastq fastq fastq	9639368480.0	60246053.0	E MTAB 13554:230324 Coated S1 L002	0:10 1:10 2:30 3:110	A:1817388578;C:1494319441;G:1527564319;T:1787447672;N:345820	10	10	30	110	1817388578	1494319441	1527564319	1787447672	345820	ERX11683773	ERS17043893	ERA27417303	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-11-20	Hatching	Embryo	Whole Organism	All anatomical structures
15012	15012	ERR12306832	ERX11683773	ERS17043893	ERP155237	PRJEB70303	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E-MTAB-13554	Transcriptome Analysis	To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule but containing a detection fluorophores. post treatment the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30	Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.	Coated	SAMEA114641726	KIS	ENA first public:2024 09 30\|External Id:SAMEA114641726\|INSDC center name:KIS\|INSDC last update:2023 11 20T16:06:50Z\|INSDC status:public\|Submitter Id:E MTAB 13554:Coated\|age:2\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 13554:Coated\|scientific name:Danio rerio\|sex:not available\|strain:transgenic lines Tgfli1:EGFPy1							10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E MTAB 13554:Coated p	Coated p	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	ILLUMINA	NextSeq 550	ERP155237	NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30	230324-Coated_S1_L001_I1_001.fastq.gz 230324-Coated_S1_L001_I2_001.fastq.gz 230324-Coated_S1_L001_R1_001.fastq.gz 230324-Coated_S1_L001_R2_001.fastq.gz	fastq fastq fastq fastq	9823147840.0	61394674.0	E MTAB 13554:230324 Coated S1 L001	0:10 1:10 2:30 3:110	A:1851113558;C:1521671335;G:1558230628;T:1822067428;N:331191	10	10	30	110	1851113558	1521671335	1558230628	1822067428	331191	ERX11683773	ERS17043893	ERA27417303	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-11-20	Hatching	Embryo	Whole Organism	All anatomical structures
15013	15013	ERR12306833	ERX11683774	ERS17043894	ERP155237	PRJEB70303	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E-MTAB-13554	Transcriptome Analysis	To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule but containing a detection fluorophores. post treatment the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30	Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.	Uncoated	SAMEA114641727	KIS	ENA first public:2024 09 30\|External Id:SAMEA114641727\|INSDC center name:KIS\|INSDC last update:2023 11 20T16:06:50Z\|INSDC status:public\|Submitter Id:E MTAB 13554:Uncoated\|age:2\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 13554:Uncoated\|scientific name:Danio rerio\|sex:not available\|strain:transgenic lines Tgfli1:EGFPy1							10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E MTAB 13554:Uncoated p	Uncoated p	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	ILLUMINA	NextSeq 550	ERP155237	NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30	230324-Uncoated_S2_L001_I1_001.fastq.gz 230324-Uncoated_S2_L001_I2_001.fastq.gz 230324-Uncoated_S2_L001_R1_001.fastq.gz 230324-Uncoated_S2_L001_R2_001.fastq.gz	fastq fastq fastq fastq	8871716800.0	55448230.0	E MTAB 13554:230324 Uncoated S2 L001	0:10 1:10 2:30 3:110	A:1718985845;C:1319560520;G:1372197713;T:1688254655;N:306567	10	10	30	110	1718985845	1319560520	1372197713	1688254655	306567	ERX11683774	ERS17043894	ERA27417303	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-11-20	Hatching	Embryo	Whole Organism	All anatomical structures
15014	15014	ERR12306830	ERX11683774	ERS17043894	ERP155237	PRJEB70303	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E-MTAB-13554	Transcriptome Analysis	To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule but containing a detection fluorophores. post treatment the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30	Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.	Uncoated	SAMEA114641727	KIS	ENA first public:2024 09 30\|External Id:SAMEA114641727\|INSDC center name:KIS\|INSDC last update:2023 11 20T16:06:50Z\|INSDC status:public\|Submitter Id:E MTAB 13554:Uncoated\|age:2\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 13554:Uncoated\|scientific name:Danio rerio\|sex:not available\|strain:transgenic lines Tgfli1:EGFPy1							10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E MTAB 13554:Uncoated p	Uncoated p	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	ILLUMINA	NextSeq 550	ERP155237	NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30	230324-Uncoated_S2_L003_I1_001.fastq.gz 230324-Uncoated_S2_L003_I2_001.fastq.gz 230324-Uncoated_S2_L003_R1_001.fastq.gz 230324-Uncoated_S2_L003_R2_001.fastq.gz	fastq fastq fastq fastq	9075478720.0	56721742.0	E MTAB 13554:230324 Uncoated S2 L003	0:10 1:10 2:30 3:110	A:1758677834;C:1349774831;G:1404463433;T:1725994897;N:480625	10	10	30	110	1758677834	1349774831	1404463433	1725994897	480625	ERX11683774	ERS17043894	ERA27417303	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-11-20	Hatching	Embryo	Whole Organism	All anatomical structures
15015	15015	ERR12306831	ERX11683774	ERS17043894	ERP155237	PRJEB70303	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E-MTAB-13554	Transcriptome Analysis	To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule but containing a detection fluorophores. post treatment the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30	Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.	Uncoated	SAMEA114641727	KIS	ENA first public:2024 09 30\|External Id:SAMEA114641727\|INSDC center name:KIS\|INSDC last update:2023 11 20T16:06:50Z\|INSDC status:public\|Submitter Id:E MTAB 13554:Uncoated\|age:2\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 13554:Uncoated\|scientific name:Danio rerio\|sex:not available\|strain:transgenic lines Tgfli1:EGFPy1							10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E MTAB 13554:Uncoated p	Uncoated p	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	ILLUMINA	NextSeq 550	ERP155237	NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30	230324-Uncoated_S2_L002_I1_001.fastq.gz 230324-Uncoated_S2_L002_I2_001.fastq.gz 230324-Uncoated_S2_L002_R1_001.fastq.gz 230324-Uncoated_S2_L002_R2_001.fastq.gz	fastq fastq fastq fastq	8705210880.0	54407568.0	E MTAB 13554:230324 Uncoated S2 L002	0:10 1:10 2:30 3:110	A:1687330583;C:1295837902;G:1345522657;T:1655826422;N:314916	10	10	30	110	1687330583	1295837902	1345522657	1655826422	314916	ERX11683774	ERS17043894	ERA27417303	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-11-20	Hatching	Embryo	Whole Organism	All anatomical structures
15016	15016	ERR12306827	ERX11683774	ERS17043894	ERP155237	PRJEB70303	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E-MTAB-13554	Transcriptome Analysis	To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule but containing a detection fluorophores. post treatment the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30	Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.	Uncoated	SAMEA114641727	KIS	ENA first public:2024 09 30\|External Id:SAMEA114641727\|INSDC center name:KIS\|INSDC last update:2023 11 20T16:06:50Z\|INSDC status:public\|Submitter Id:E MTAB 13554:Uncoated\|age:2\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 13554:Uncoated\|scientific name:Danio rerio\|sex:not available\|strain:transgenic lines Tgfli1:EGFPy1							10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E MTAB 13554:Uncoated p	Uncoated p	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	ILLUMINA	NextSeq 550	ERP155237	NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30	230324-Uncoated_S2_L004_I1_001.fastq.gz 230324-Uncoated_S2_L004_I2_001.fastq.gz 230324-Uncoated_S2_L004_R1_001.fastq.gz 230324-Uncoated_S2_L004_R2_001.fastq.gz	fastq fastq fastq fastq	8846203360.0	55288771.0	E MTAB 13554:230324 Uncoated S2 L004	0:10 1:10 2:30 3:110	A:1715100047;C:1316853239;G:1367208350;T:1682248092;N:355082	10	10	30	110	1715100047	1316853239	1367208350	1682248092	355082	ERX11683774	ERS17043894	ERA27417303	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-11-20	Hatching	Embryo	Whole Organism	All anatomical structures
24656	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

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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");;