metadata: run_metadata: 513 rows where experiment.library_selection = "cDNA" and tissue

513 rows where experiment.library_selection = "cDNA" and tissue_curation = "Blood"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	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
24784	24784	SRR25502048	SRX21232930	SRS18488024	SRP453114	PRJNA1001808	The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger	GSE239949	Transcriptome Analysis	From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.	pubmed:28382966	Sample 15 05316 MCK mut3	GSM7678168	tissue:lyz+ mpx+ granulocytes\|cell type:lyz+ mpx+ granulocytes\|genotype:zbtb11 mutant mne\|age:48 hpf\|geo loc name:missing\|collection date:missing	Sample 15 05316 MCK mut3	Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample	lyz+ mpx+ granulocytes		RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.		cell type:lyz+ mpx+ granulocytes\|genotype:zbtb11 mutant mne\|age:48 hpf	GSM7678168	GSM7678168: Sample 15 05316 MCK mut3; Danio rerio; RNA Seq	GSM7678168 r1	GSM7678168	1	RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP453114		15-05316_MCK_mut3_GTGCTT_L002_R1_001.fastq.gz 15-05316_MCK_mut3_GTGCTT_L002_R2_001.fastq.gz	fastq fastq	4329868620.0	20618422.0	GSM7678168 r1	0:105 1:105	A:1075032412;C:1077085067;G:1119735718;T:1057797736;N:217687	105	105			1075032412	1077085067	1119735718	1057797736	217687	SRX21232930	SRS18488024	SRA1685493	Rural Clinical Sciences, La Trobe University	Rural Clinical Sciences, La Trobe University	2	0.78961	0.91048	0.20166	0.23232	0.81556	0.81115	0.59478	0.59379	105	105	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-08-03	Hatching	Embryo	Blood	Hematopoietic System
24785	24785	SRR25502049	SRX21232929	SRS18488023	SRP453114	PRJNA1001808	The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger	GSE239949	Transcriptome Analysis	From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.	pubmed:28382966	Sample 15 05316 MCK mut2	GSM7678167	tissue:lyz+ mpx+ granulocytes\|cell type:lyz+ mpx+ granulocytes\|genotype:zbtb11 mutant mne\|age:48 hpf\|geo loc name:missing\|collection date:missing	Sample 15 05316 MCK mut2	Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample	lyz+ mpx+ granulocytes		RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.		cell type:lyz+ mpx+ granulocytes\|genotype:zbtb11 mutant mne\|age:48 hpf	GSM7678167	GSM7678167: Sample 15 05316 MCK mut2; Danio rerio; RNA Seq	GSM7678167 r1	GSM7678167	1	RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP453114		15-05316_MCK_mut2_ACCTCA_L002_R1_001.fastq.gz 15-05316_MCK_mut2_ACCTCA_L002_R2_001.fastq.gz	fastq fastq	4444374270.0	21163687.0	GSM7678167 r1	0:105 1:105	A:1114919906;C:1098541058;G:1145427151;T:1085262902;N:223253	105	105			1114919906	1098541058	1145427151	1085262902	223253	SRX21232929	SRS18488023	SRA1685493	Rural Clinical Sciences, La Trobe University	Rural Clinical Sciences, La Trobe University	2	0.74961	0.90068	0.18596	0.22057	0.81115	0.80754	0.5829	0.58615	105	105	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-08-03	Hatching	Embryo	Blood	Hematopoietic System
24786	24786	SRR25502050	SRX21232928	SRS18488022	SRP453114	PRJNA1001808	The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger	GSE239949	Transcriptome Analysis	From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.	pubmed:28382966	Sample 15 05316 MCK mut1	GSM7678166	tissue:lyz+ mpx+ granulocytes\|cell type:lyz+ mpx+ granulocytes\|genotype:zbtb11 mutant mne\|age:48 hpf\|geo loc name:missing\|collection date:missing	Sample 15 05316 MCK mut1	Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample	lyz+ mpx+ granulocytes		RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.		cell type:lyz+ mpx+ granulocytes\|genotype:zbtb11 mutant mne\|age:48 hpf	GSM7678166	GSM7678166: Sample 15 05316 MCK mut1; Danio rerio; RNA Seq	GSM7678166 r1	GSM7678166	1	RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP453114		15-05316_MCK_mut1_GCACTA_L002_R1_001.fastq.gz 15-05316_MCK_mut1_GCACTA_L002_R2_001.fastq.gz	fastq fastq	4459467180.0	21235558.0	GSM7678166 r1	0:105 1:105	A:1206908747;C:1012207561;G:1060393698;T:1179731376;N:225798	105	105			1206908747	1012207561	1060393698	1179731376	225798	SRX21232928	SRS18488022	SRA1685493	Rural Clinical Sciences, La Trobe University	Rural Clinical Sciences, La Trobe University	2	0.75719	0.88462	0.20719	0.24095	0.78559	0.77914	0.50538	0.55691	105	105	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-08-03	Hatching	Embryo	Blood	Hematopoietic System
24787	24787	SRR25502051	SRX21232927	SRS18488021	SRP453114	PRJNA1001808	The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger	GSE239949	Transcriptome Analysis	From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.	pubmed:28382966	Sample 15 05315 MCK WT3	GSM7678165	tissue:lyz+ mpx+ granulocytes\|cell type:lyz+ mpx+ granulocytes\|genotype:wild type\|age:48 hpf\|geo loc name:missing\|collection date:missing	Sample 15 05315 MCK WT3	Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample	lyz+ mpx+ granulocytes		RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.		cell type:lyz+ mpx+ granulocytes\|genotype:wild type\|age:48 hpf	GSM7678165	GSM7678165: Sample 15 05315 MCK WT3; Danio rerio; RNA Seq	GSM7678165 r1	GSM7678165	1	RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP453114		15-05315_MCK_WT3_AGTGAG_L002_R1_001.fastq.gz 15-05315_MCK_WT3_AGTGAG_L002_R2_001.fastq.gz	fastq fastq	3925329240.0	18692044.0	GSM7678165 r1	0:105 1:105	A:1022654212;C:930239389;G:973328942;T:998905803;N:200894	105	105			1022654212	930239389	973328942	998905803	200894	SRX21232927	SRS18488021	SRA1685493	Rural Clinical Sciences, La Trobe University	Rural Clinical Sciences, La Trobe University	2	0.75647	0.89377	0.19165	0.22718	0.81057	0.80501	0.51173	0.54819	105	105	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-08-03	Hatching	Embryo	Blood	Hematopoietic System
24788	24788	SRR25502052	SRX21232926	SRS18488020	SRP453114	PRJNA1001808	The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger	GSE239949	Transcriptome Analysis	From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.	pubmed:28382966	Sample 15 05314 MCK WT2	GSM7678164	tissue:lyz+ mpx+ granulocytes\|cell type:lyz+ mpx+ granulocytes\|genotype:wild type\|age:48 hpf\|geo loc name:missing\|collection date:missing	Sample 15 05314 MCK WT2	Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample	lyz+ mpx+ granulocytes		RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.		cell type:lyz+ mpx+ granulocytes\|genotype:wild type\|age:48 hpf	GSM7678164	GSM7678164: Sample 15 05314 MCK WT2; Danio rerio; RNA Seq	GSM7678164 r1	GSM7678164	1	RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP453114		15-05314_MCK_WT2_TGGTGA_L002_R2_001.fastq.gz 15-05314_MCK_WT2_TGGTGA_L002_R1_001.fastq.gz	fastq fastq	4100489820.0	19526142.0	GSM7678164 r1	0:105 1:105	A:1022482319;C:1016090490;G:1063619365;T:998086417;N:211229	105	105			1022482319	1016090490	1063619365	998086417	211229	SRX21232926	SRS18488020	SRA1685493	Rural Clinical Sciences, La Trobe University	Rural Clinical Sciences, La Trobe University	2	0.76378	0.90522	0.20093	0.23619	0.82467	0.82049	0.57261	0.562	105	105	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-08-03	Hatching	Embryo	Blood	Hematopoietic System
24789	24789	SRR25502053	SRX21232925	SRS18488019	SRP453114	PRJNA1001808	The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger	GSE239949	Transcriptome Analysis	From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.	pubmed:28382966	Sample 15 05313 MCK WT1	GSM7678163	tissue:lyz+ mpx+ granulocytes\|cell type:lyz+ mpx+ granulocytes\|genotype:wild type\|age:48 hpf\|geo loc name:missing\|collection date:missing	Sample 15 05313 MCK WT1	Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample	lyz+ mpx+ granulocytes		RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.		cell type:lyz+ mpx+ granulocytes\|genotype:wild type\|age:48 hpf	GSM7678163	GSM7678163: Sample 15 05313 MCK WT1; Danio rerio; RNA Seq	GSM7678163 r1	GSM7678163	1	RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP453114		15-05313_MCK_WT1_AACCAG_L002_R1_001.fastq.gz 15-05313_MCK_WT1_AACCAG_L002_R2_001.fastq.gz	fastq fastq	4135721100.0	19693910.0	GSM7678163 r1	0:105 1:105	A:1048700719;C:1014162128;G:1070155053;T:1002495763;N:207437	105	105			1048700719	1014162128	1070155053	1002495763	207437	SRX21232925	SRS18488019	SRA1685493	Rural Clinical Sciences, La Trobe University	Rural Clinical Sciences, La Trobe University	2	0.70974	0.9073	0.1771	0.22534	0.82483	0.81625	0.56311	0.55183	105	105	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-08-03	Hatching	Embryo	Blood	Hematopoietic System
28389	28389	SRR26213385	SRX21923919	SRS19008430	SRP463773	PRJNA1022165	Transcriptomic analysis of Per2 deficient neutrophils compared WT neutrophils following infection.	GSE244308	Transcriptome Analysis	Functional analysis demonstrates that neutrophils deficient in Per2 have reduced bactericidal activity when compared WT neutrophils. Overall design: Differential gene expression analysis of RNA seq data from Per2 deficient neutrophils and WT neutrophils post Salmonella typhimurium infection in biological quadruplet.		Neutrophils WT infected 4	GSM7813285	tissue:Neutrophil\|developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2/WT\|infection:Salm1lla typhimurium\|geo loc name:missing\|collection date:missing	Neutrophils WT infected 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyze the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz10 Supplementary files format and content: Comma separated values file show FPKM Log2FC and adj P value of DEGs comparing Per2Infected and WTInfected samples.	Neutrophil	At 52 hpf 4 hours post lights on Tglyz:DsRED2/WT and Tglyz:DsRED2;per2 / zebrafish larvae we infected with 1 000 CFU Salmonella Typhimurium and neutrophils were isolated at 3 hours post infection by FACS.	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C under standard light:dark conditions	developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2/WT\|infection:Salm1lla typhimurium	GSM7813285	GSM7813285: Neutrophils WT infected 4; Danio rerio; RNA Seq	GSM7813285 r1	GSM7813285	1	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP463773	loader:fastq load.py	WTInfected-4_S8_R1_001.fastq.gz	fastq	2240130033.0	29683768.0	GSM7813285 r1	0:75.47	A:639465198;C:479506246;G:493408026;T:627654835;N:95728	75				639465198	479506246	493408026	627654835	95728	SRX21923919	SRS19008430	SRA1722831	The University of Auckland	The University of Auckland	1	0.89082		0.28084		0.75523		0.4978		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2023-09-28	Larval	Larval	Blood	Hematopoietic System
28390	28390	SRR26213386	SRX21923918	SRS19008429	SRP463773	PRJNA1022165	Transcriptomic analysis of Per2 deficient neutrophils compared WT neutrophils following infection.	GSE244308	Transcriptome Analysis	Functional analysis demonstrates that neutrophils deficient in Per2 have reduced bactericidal activity when compared WT neutrophils. Overall design: Differential gene expression analysis of RNA seq data from Per2 deficient neutrophils and WT neutrophils post Salmonella typhimurium infection in biological quadruplet.		Neutrophils WT infected 3	GSM7813284	tissue:Neutrophil\|developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2/WT\|infection:Salm1lla typhimurium\|geo loc name:missing\|collection date:missing	Neutrophils WT infected 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyze the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz10 Supplementary files format and content: Comma separated values file show FPKM Log2FC and adj P value of DEGs comparing Per2Infected and WTInfected samples.	Neutrophil	At 52 hpf 4 hours post lights on Tglyz:DsRED2/WT and Tglyz:DsRED2;per2 / zebrafish larvae we infected with 1 000 CFU Salmonella Typhimurium and neutrophils were isolated at 3 hours post infection by FACS.	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C under standard light:dark conditions	developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2/WT\|infection:Salm1lla typhimurium	GSM7813284	GSM7813284: Neutrophils WT infected 3; Danio rerio; RNA Seq	GSM7813284 r1	GSM7813284	1	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP463773	loader:fastq load.py	WTInfected-3_S7_R1_001.fastq.gz	fastq	2789643441.0	37059064.0	GSM7813284 r1	0:75.28	A:770315857;C:626379098;G:642210747;T:750373702;N:364037	75				770315857	626379098	642210747	750373702	364037	SRX21923918	SRS19008429	SRA1722831	The University of Auckland	The University of Auckland	1	0.89494		0.12907		0.81154		0.50044		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2023-09-28	Larval	Larval	Blood	Hematopoietic System
28391	28391	SRR26213387	SRX21923917	SRS19008428	SRP463773	PRJNA1022165	Transcriptomic analysis of Per2 deficient neutrophils compared WT neutrophils following infection.	GSE244308	Transcriptome Analysis	Functional analysis demonstrates that neutrophils deficient in Per2 have reduced bactericidal activity when compared WT neutrophils. Overall design: Differential gene expression analysis of RNA seq data from Per2 deficient neutrophils and WT neutrophils post Salmonella typhimurium infection in biological quadruplet.		Neutrophils WT infected 2	GSM7813283	tissue:Neutrophil\|developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2/WT\|infection:Salm1lla typhimurium\|geo loc name:missing\|collection date:missing	Neutrophils WT infected 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyze the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz10 Supplementary files format and content: Comma separated values file show FPKM Log2FC and adj P value of DEGs comparing Per2Infected and WTInfected samples.	Neutrophil	At 52 hpf 4 hours post lights on Tglyz:DsRED2/WT and Tglyz:DsRED2;per2 / zebrafish larvae we infected with 1 000 CFU Salmonella Typhimurium and neutrophils were isolated at 3 hours post infection by FACS.	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C under standard light:dark conditions	developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2/WT\|infection:Salm1lla typhimurium	GSM7813283	GSM7813283: Neutrophils WT infected 2; Danio rerio; RNA Seq	GSM7813283 r1	GSM7813283	1	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP463773	loader:fastq load.py	WTInfected-2_S6_R1_001.fastq.gz	fastq	2502579643.0	33171064.0	GSM7813283 r1	0:75.44	A:690295075;C:562877524;G:577315919;T:671999174;N:91951	75				690295075	562877524	577315919	671999174	91951	SRX21923917	SRS19008428	SRA1722831	The University of Auckland	The University of Auckland	1	0.89596		0.11653		0.82562		0.47762		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2023-09-28	Larval	Larval	Blood	Hematopoietic System
28392	28392	SRR26213388	SRX21923916	SRS19008427	SRP463773	PRJNA1022165	Transcriptomic analysis of Per2 deficient neutrophils compared WT neutrophils following infection.	GSE244308	Transcriptome Analysis	Functional analysis demonstrates that neutrophils deficient in Per2 have reduced bactericidal activity when compared WT neutrophils. Overall design: Differential gene expression analysis of RNA seq data from Per2 deficient neutrophils and WT neutrophils post Salmonella typhimurium infection in biological quadruplet.		Neutrophils WT infected 1	GSM7813282	tissue:Neutrophil\|developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2/WT\|infection:Salm1lla typhimurium\|geo loc name:missing\|collection date:missing	Neutrophils WT infected 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyze the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz10 Supplementary files format and content: Comma separated values file show FPKM Log2FC and adj P value of DEGs comparing Per2Infected and WTInfected samples.	Neutrophil	At 52 hpf 4 hours post lights on Tglyz:DsRED2/WT and Tglyz:DsRED2;per2 / zebrafish larvae we infected with 1 000 CFU Salmonella Typhimurium and neutrophils were isolated at 3 hours post infection by FACS.	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C under standard light:dark conditions	developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2/WT\|infection:Salm1lla typhimurium	GSM7813282	GSM7813282: Neutrophils WT infected 1; Danio rerio; RNA Seq	GSM7813282 r1	GSM7813282	1	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP463773	loader:fastq load.py	WTInfected-1_S5_R1_001.fastq.gz	fastq	2629109363.0	34890907.0	GSM7813282 r1	0:75.35	A:717313087;C:596048245;G:613729475;T:701790568;N:227988	75				717313087	596048245	613729475	701790568	227988	SRX21923916	SRS19008427	SRA1722831	The University of Auckland	The University of Auckland	1	0.88964		0.13171		0.81142		0.49273		73		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2023-09-28	Larval	Larval	Blood	Hematopoietic System
28393	28393	SRR26213389	SRX21923915	SRS19008426	SRP463773	PRJNA1022165	Transcriptomic analysis of Per2 deficient neutrophils compared WT neutrophils following infection.	GSE244308	Transcriptome Analysis	Functional analysis demonstrates that neutrophils deficient in Per2 have reduced bactericidal activity when compared WT neutrophils. Overall design: Differential gene expression analysis of RNA seq data from Per2 deficient neutrophils and WT neutrophils post Salmonella typhimurium infection in biological quadruplet.		Neutrophils per2 infected 4	GSM7813281	tissue:Neutrophil\|developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2;per2 / \|infection:Salm1lla typhimurium\|geo loc name:missing\|collection date:missing	Neutrophils per2 infected 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyze the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz10 Supplementary files format and content: Comma separated values file show FPKM Log2FC and adj P value of DEGs comparing Per2Infected and WTInfected samples.	Neutrophil	At 52 hpf 4 hours post lights on Tglyz:DsRED2/WT and Tglyz:DsRED2;per2 / zebrafish larvae we infected with 1 000 CFU Salmonella Typhimurium and neutrophils were isolated at 3 hours post infection by FACS.	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C under standard light:dark conditions	developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2;per2 / \|infection:Salm1lla typhimurium	GSM7813281	GSM7813281: Neutrophils per2 infected 4; Danio rerio; RNA Seq	GSM7813281 r1	GSM7813281	1	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP463773	loader:fastq load.py	per2Infected-4_S16_R1_001.fastq.gz	fastq	2915831120.0	38708122.0	GSM7813281 r1	0:75.33	A:819771092;C:637630362;G:654348519;T:803699649;N:381498	75				819771092	637630362	654348519	803699649	381498	SRX21923915	SRS19008426	SRA1722831	The University of Auckland	The University of Auckland	1	0.90568		0.15837		0.82055		0.49547		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2023-09-28	Larval	Larval	Blood	Hematopoietic System
28394	28394	SRR26213390	SRX21923914	SRS19008425	SRP463773	PRJNA1022165	Transcriptomic analysis of Per2 deficient neutrophils compared WT neutrophils following infection.	GSE244308	Transcriptome Analysis	Functional analysis demonstrates that neutrophils deficient in Per2 have reduced bactericidal activity when compared WT neutrophils. Overall design: Differential gene expression analysis of RNA seq data from Per2 deficient neutrophils and WT neutrophils post Salmonella typhimurium infection in biological quadruplet.		Neutrophils per2 infected 3	GSM7813280	tissue:Neutrophil\|developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2;per2 / \|infection:Salm1lla typhimurium\|geo loc name:missing\|collection date:missing	Neutrophils per2 infected 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyze the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz10 Supplementary files format and content: Comma separated values file show FPKM Log2FC and adj P value of DEGs comparing Per2Infected and WTInfected samples.	Neutrophil	At 52 hpf 4 hours post lights on Tglyz:DsRED2/WT and Tglyz:DsRED2;per2 / zebrafish larvae we infected with 1 000 CFU Salmonella Typhimurium and neutrophils were isolated at 3 hours post infection by FACS.	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C under standard light:dark conditions	developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2;per2 / \|infection:Salm1lla typhimurium	GSM7813280	GSM7813280: Neutrophils per2 infected 3; Danio rerio; RNA Seq	GSM7813280 r1	GSM7813280	1	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP463773	loader:fastq load.py	per2Infected-3_S15_R1_001.fastq.gz	fastq	2622630688.0	34745018.0	GSM7813280 r1	0:75.48	A:726047024;C:584906297;G:600999032;T:710582433;N:95902	75				726047024	584906297	600999032	710582433	95902	SRX21923914	SRS19008425	SRA1722831	The University of Auckland	The University of Auckland	1	0.91129		0.1229		0.81345		0.48284		75		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2023-09-28	Larval	Larval	Blood	Hematopoietic System
28395	28395	SRR26213391	SRX21923913	SRS19008424	SRP463773	PRJNA1022165	Transcriptomic analysis of Per2 deficient neutrophils compared WT neutrophils following infection.	GSE244308	Transcriptome Analysis	Functional analysis demonstrates that neutrophils deficient in Per2 have reduced bactericidal activity when compared WT neutrophils. Overall design: Differential gene expression analysis of RNA seq data from Per2 deficient neutrophils and WT neutrophils post Salmonella typhimurium infection in biological quadruplet.		Neutrophils per2 infected 2	GSM7813279	tissue:Neutrophil\|developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2;per2 / \|infection:Salm1lla typhimurium\|geo loc name:missing\|collection date:missing	Neutrophils per2 infected 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyze the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz10 Supplementary files format and content: Comma separated values file show FPKM Log2FC and adj P value of DEGs comparing Per2Infected and WTInfected samples.	Neutrophil	At 52 hpf 4 hours post lights on Tglyz:DsRED2/WT and Tglyz:DsRED2;per2 / zebrafish larvae we infected with 1 000 CFU Salmonella Typhimurium and neutrophils were isolated at 3 hours post infection by FACS.	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C under standard light:dark conditions	developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2;per2 / \|infection:Salm1lla typhimurium	GSM7813279	GSM7813279: Neutrophils per2 infected 2; Danio rerio; RNA Seq	GSM7813279 r1	GSM7813279	1	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP463773	loader:fastq load.py	per2Infected-2_S14_R1_001.fastq.gz	fastq	2152892336.0	28547218.0	GSM7813279 r1	0:75.42	A:594950127;C:480727855;G:495163350;T:581915730;N:135274	75				594950127	480727855	495163350	581915730	135274	SRX21923913	SRS19008424	SRA1722831	The University of Auckland	The University of Auckland	1	0.9068		0.11944		0.82804		0.48956		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2023-09-28	Larval	Larval	Blood	Hematopoietic System
28396	28396	SRR26213392	SRX21923912	SRS19008423	SRP463773	PRJNA1022165	Transcriptomic analysis of Per2 deficient neutrophils compared WT neutrophils following infection.	GSE244308	Transcriptome Analysis	Functional analysis demonstrates that neutrophils deficient in Per2 have reduced bactericidal activity when compared WT neutrophils. Overall design: Differential gene expression analysis of RNA seq data from Per2 deficient neutrophils and WT neutrophils post Salmonella typhimurium infection in biological quadruplet.		Neutrophils per2 infected 1	GSM7813278	tissue:Neutrophil\|developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2;per2 / \|infection:Salm1lla typhimurium\|geo loc name:missing\|collection date:missing	Neutrophils per2 infected 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyze the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz10 Supplementary files format and content: Comma separated values file show FPKM Log2FC and adj P value of DEGs comparing Per2Infected and WTInfected samples.	Neutrophil	At 52 hpf 4 hours post lights on Tglyz:DsRED2/WT and Tglyz:DsRED2;per2 / zebrafish larvae we infected with 1 000 CFU Salmonella Typhimurium and neutrophils were isolated at 3 hours post infection by FACS.	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C under standard light:dark conditions	developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2;per2 / \|infection:Salm1lla typhimurium	GSM7813278	GSM7813278: Neutrophils per2 infected 1; Danio rerio; RNA Seq	GSM7813278 r1	GSM7813278	1	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP463773	loader:fastq load.py	per2Infcted-1_S13_R1_001.fastq.gz	fastq	2276537599.0	30215018.0	GSM7813278 r1	0:75.34	A:614225653;C:523562022;G:541795396;T:596817124;N:137404	75				614225653	523562022	541795396	596817124	137404	SRX21923912	SRS19008423	SRA1722831	The University of Auckland	The University of Auckland	1	0.92361		0.09247		0.81324		0.46862		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2023-09-28	Larval	Larval	Blood	Hematopoietic System
28902	28902	SRR26827532	SRX22524052	SRS19535497	SRP471831	PRJNA1040223	The Caudal Hematopoietic Tissue is Differentially Required for Erythrocytes and Neutrophils from Definitive Hematopoiesis in Zebrafish	GSE247730	Transcriptome Analysis	Neutrophils and erythrocytes are vital to the immune system and oxygen transport respectively. However the mechanisms by which hematopoietic niches support their development remain incompletely understood. In hematopoiesis research zebrafish larvae are a common model for studying the development of definitive neutrophils and erythrocytes in the caudal hematopoietic tissue. In this study we showed that erythrocytes predominantly reside inside the blood vessels of the CHT while neutrophils stay outside. Ectopic vascular endothelium induced by Bone Morphogenetic Protein 2bBmp2b overexpression attracts both cell types with erythrocytes inside and neutrophils outside. CHT removal has minimal impact on definitive neutrophils from the ventral wall of the dorsal aorta VDA but severely affects definitive erythrocytes from the same source. Bulk RNA sequencing identified epoa as a vital factor for erythrocyte generation within CHT endothelium. Overexpression of epoa through the lyve1b promoter which is specifically expressed in vein lymphatic vessels and CHT vein endothelial cells rescued the erythrocyte reduction in epoa mutants. Our study reveals that the caudal hematopoietic tissue is differentially required for definitive erythrocytes and neutrophils. Overall design: We then performed gene expression profiling analysis using data obtained from BULK RNA seq of 5dpf vein endothelium cells and endothelium cells.		vein endothelium cells Day5 rep2	GSM7899809	source name:Caudal hematopoietic tissue\|tissue:Caudal hematopoietic tissue\|cell type:vein endothelium cells\|genotype:Wildtype\|treatment:no treatment\|geo loc name:missing\|collection date:missing	vein endothelium cells Day5 rep2	Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value≤20 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 with “ rna strandness RF” and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments Principal component analysis PCA was performed with R package gmodels http://www.r project.org/ in this experience;RNAs differential expression analysis was performed by DESeq2; Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample	Caudal hematopoietic tissue		Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.		tissue:Caudal hematopoietic tissue\|cell type:vein endothelium cells\|genotype:Wildtype\|treatment:no treatment	GSM7899809	GSM7899809: vein endothelium cells Day5 rep2; Danio rerio; RNA Seq	GSM7899809 r1	GSM7899809	1	Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP471831	loader:fastq load.py	vein_endothelium_cells-2_1.fq.gz vein_endothelium_cells-2_2.fq.gz	fastq fastq	9110989800.0	30369966.0	GSM7899809 r1	0:150 1:150	A:2454542720;C:2090617752;G:2126374129;T:2439172440;N:282759	150	150			2454542720	2090617752	2126374129	2439172440	282759	SRX22524052	SRS19535497	SRA1750986	South China University of Technology	South China University of Technology	2	0.89413	0.89048	0.1507	0.14922	0.78466	0.78496	0.5263	0.5335	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2023-11-14	Larval	Larval	Blood	Hematopoietic System
28903	28903	SRR26827533	SRX22524051	SRS19535496	SRP471831	PRJNA1040223	The Caudal Hematopoietic Tissue is Differentially Required for Erythrocytes and Neutrophils from Definitive Hematopoiesis in Zebrafish	GSE247730	Transcriptome Analysis	Neutrophils and erythrocytes are vital to the immune system and oxygen transport respectively. However the mechanisms by which hematopoietic niches support their development remain incompletely understood. In hematopoiesis research zebrafish larvae are a common model for studying the development of definitive neutrophils and erythrocytes in the caudal hematopoietic tissue. In this study we showed that erythrocytes predominantly reside inside the blood vessels of the CHT while neutrophils stay outside. Ectopic vascular endothelium induced by Bone Morphogenetic Protein 2bBmp2b overexpression attracts both cell types with erythrocytes inside and neutrophils outside. CHT removal has minimal impact on definitive neutrophils from the ventral wall of the dorsal aorta VDA but severely affects definitive erythrocytes from the same source. Bulk RNA sequencing identified epoa as a vital factor for erythrocyte generation within CHT endothelium. Overexpression of epoa through the lyve1b promoter which is specifically expressed in vein lymphatic vessels and CHT vein endothelial cells rescued the erythrocyte reduction in epoa mutants. Our study reveals that the caudal hematopoietic tissue is differentially required for definitive erythrocytes and neutrophils. Overall design: We then performed gene expression profiling analysis using data obtained from BULK RNA seq of 5dpf vein endothelium cells and endothelium cells.		vein endothelium cells Day5 rep1	GSM7899808	source name:Caudal hematopoietic tissue\|tissue:Caudal hematopoietic tissue\|cell type:vein endothelium cells\|genotype:Wildtype\|treatment:no treatment\|geo loc name:missing\|collection date:missing	vein endothelium cells Day5 rep1	Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value≤20 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 with “ rna strandness RF” and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments Principal component analysis PCA was performed with R package gmodels http://www.r project.org/ in this experience;RNAs differential expression analysis was performed by DESeq2; Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample	Caudal hematopoietic tissue		Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.		tissue:Caudal hematopoietic tissue\|cell type:vein endothelium cells\|genotype:Wildtype\|treatment:no treatment	GSM7899808	GSM7899808: vein endothelium cells Day5 rep1; Danio rerio; RNA Seq	GSM7899808 r1	GSM7899808	1	Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP471831	loader:fastq load.py	vein_endothelium_cells-1_2.fq.gz vein_endothelium_cells-1_1.fq.gz	fastq fastq	8585973300.0	28619911.0	GSM7899808 r1	0:150 1:150	A:2253650188;C:2015841518;G:2037568162;T:2278266858;N:646574	150	150			2253650188	2015841518	2037568162	2278266858	646574	SRX22524051	SRS19535496	SRA1750986	South China University of Technology	South China University of Technology	2	0.8876	0.88392	0.14777	0.14719	0.78969	0.79038	0.53142	0.53136	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2023-11-14	Larval	Larval	Blood	Hematopoietic System
28904	28904	SRR26827534	SRX22524050	SRS19535495	SRP471831	PRJNA1040223	The Caudal Hematopoietic Tissue is Differentially Required for Erythrocytes and Neutrophils from Definitive Hematopoiesis in Zebrafish	GSE247730	Transcriptome Analysis	Neutrophils and erythrocytes are vital to the immune system and oxygen transport respectively. However the mechanisms by which hematopoietic niches support their development remain incompletely understood. In hematopoiesis research zebrafish larvae are a common model for studying the development of definitive neutrophils and erythrocytes in the caudal hematopoietic tissue. In this study we showed that erythrocytes predominantly reside inside the blood vessels of the CHT while neutrophils stay outside. Ectopic vascular endothelium induced by Bone Morphogenetic Protein 2bBmp2b overexpression attracts both cell types with erythrocytes inside and neutrophils outside. CHT removal has minimal impact on definitive neutrophils from the ventral wall of the dorsal aorta VDA but severely affects definitive erythrocytes from the same source. Bulk RNA sequencing identified epoa as a vital factor for erythrocyte generation within CHT endothelium. Overexpression of epoa through the lyve1b promoter which is specifically expressed in vein lymphatic vessels and CHT vein endothelial cells rescued the erythrocyte reduction in epoa mutants. Our study reveals that the caudal hematopoietic tissue is differentially required for definitive erythrocytes and neutrophils. Overall design: We then performed gene expression profiling analysis using data obtained from BULK RNA seq of 5dpf vein endothelium cells and endothelium cells.		non vein endothelium cells Control Day5 rep2	GSM7899807	source name:Caudal hematopoietic tissue\|tissue:Caudal hematopoietic tissue\|cell type:non vein endothelium cells\|genotype:Wildtype\|treatment:no treatment\|geo loc name:missing\|collection date:missing	non vein endothelium cells Control Day5 rep2	Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value≤20 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 with “ rna strandness RF” and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments Principal component analysis PCA was performed with R package gmodels http://www.r project.org/ in this experience;RNAs differential expression analysis was performed by DESeq2; Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample	Caudal hematopoietic tissue		Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.		tissue:Caudal hematopoietic tissue\|cell type:non vein endothelium cells\|genotype:Wildtype\|treatment:no treatment	GSM7899807	GSM7899807: non vein endothelium cells Control Day5 rep2; Danio rerio; RNA Seq	GSM7899807 r1	GSM7899807	1	Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP471831	loader:fastq load.py	non-vein_endothelium_cells-2_1.fq.gz non-vein_endothelium_cells-2_2.fq.gz	fastq fastq	9363942600.0	31213142.0	GSM7899807 r1	0:150 1:150	A:2523111369;C:2155598161;G:2171776473;T:2513164552;N:292045	150	150			2523111369	2155598161	2171776473	2513164552	292045	SRX22524050	SRS19535495	SRA1750986	South China University of Technology	South China University of Technology	2	0.93879	0.93706	0.10971	0.10945	0.76721	0.76737	0.51346	0.51513	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2023-11-14	Larval	Larval	Blood	Hematopoietic System
28905	28905	SRR26827535	SRX22524049	SRS19535494	SRP471831	PRJNA1040223	The Caudal Hematopoietic Tissue is Differentially Required for Erythrocytes and Neutrophils from Definitive Hematopoiesis in Zebrafish	GSE247730	Transcriptome Analysis	Neutrophils and erythrocytes are vital to the immune system and oxygen transport respectively. However the mechanisms by which hematopoietic niches support their development remain incompletely understood. In hematopoiesis research zebrafish larvae are a common model for studying the development of definitive neutrophils and erythrocytes in the caudal hematopoietic tissue. In this study we showed that erythrocytes predominantly reside inside the blood vessels of the CHT while neutrophils stay outside. Ectopic vascular endothelium induced by Bone Morphogenetic Protein 2bBmp2b overexpression attracts both cell types with erythrocytes inside and neutrophils outside. CHT removal has minimal impact on definitive neutrophils from the ventral wall of the dorsal aorta VDA but severely affects definitive erythrocytes from the same source. Bulk RNA sequencing identified epoa as a vital factor for erythrocyte generation within CHT endothelium. Overexpression of epoa through the lyve1b promoter which is specifically expressed in vein lymphatic vessels and CHT vein endothelial cells rescued the erythrocyte reduction in epoa mutants. Our study reveals that the caudal hematopoietic tissue is differentially required for definitive erythrocytes and neutrophils. Overall design: We then performed gene expression profiling analysis using data obtained from BULK RNA seq of 5dpf vein endothelium cells and endothelium cells.		non vein endothelium cells Control Day5 rep1	GSM7899806	source name:Caudal hematopoietic tissue\|tissue:Caudal hematopoietic tissue\|cell type:non vein endothelium cells\|genotype:Wildtype\|treatment:no treatment\|geo loc name:missing\|collection date:missing	non vein endothelium cells Control Day5 rep1	Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value≤20 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 with “ rna strandness RF” and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments Principal component analysis PCA was performed with R package gmodels http://www.r project.org/ in this experience;RNAs differential expression analysis was performed by DESeq2; Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample	Caudal hematopoietic tissue		Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.		tissue:Caudal hematopoietic tissue\|cell type:non vein endothelium cells\|genotype:Wildtype\|treatment:no treatment	GSM7899806	GSM7899806: non vein endothelium cells Control Day5 rep1; Danio rerio; RNA Seq	GSM7899806 r1	GSM7899806	1	Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP471831	loader:fastq load.py	non-vein_endothelium_cells-1_1.fq.gz non-vein_endothelium_cells-1_2.fq.gz	fastq fastq	8396176800.0	27987256.0	GSM7899806 r1	0:150 1:150	A:2190594419;C:1990596503;G:2019391921;T:2194713332;N:880625	150	150			2190594419	1990596503	2019391921	2194713332	880625	SRX22524049	SRS19535494	SRA1750986	South China University of Technology	South China University of Technology	2	0.94508	0.94385	0.0967	0.09697	0.77642	0.77632	0.49896	0.49962	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2023-11-14	Larval	Larval	Blood	Hematopoietic System
29175	29175	SRR27292304	SRX22969963	SRS19936063	SRP479046	PRJNA1054617	Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish	GSE250610	Transcriptome Analysis	Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…	pubmed:38922186	Burned Larval Zebrafish 48 hours post burn	GSM7982886	source name:Whole blood\|tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Burn\|geo loc name:missing\|collection date:missing	Burned Larval Zebrafish 48 hours post burn	FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix	Whole blood	Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.	tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Burn	GSM7982886	GSM7982886: Burned Larval Zebrafish 48 hours post burn; Danio rerio; RNA Seq	GSM7982886 r1	GSM7982886	1	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP479046	loader:fastq load.py	Burn-48hpb_S5_L001_R2_001.fastq.gz Burn-48hpb_S5_L001_R1_001.fastq.gz	fastq fastq	20874980529.0	178418637.0	GSM7982886 r1	0:28 1:89	A:5945091269;C:4392590896;G:4497688824;T:6035946283;N:3663257	28	89			5945091269	4392590896	4497688824	6035946283	3663257	SRX22969963	SRS19936063	SRA1772557	University of Wisconsin-Madison	University of Wisconsin-Madison	2	0.00573	0.91666	0.00222	0.19474	0.9931	0.79306	0.42082	0.53801	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2023-12-19	Multi-stage	Multi-stage	Blood	Hematopoietic System
29176	29176	SRR27292305	SRX22969963	SRS19936063	SRP479046	PRJNA1054617	Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish	GSE250610	Transcriptome Analysis	Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…	pubmed:38922186	Burned Larval Zebrafish 48 hours post burn	GSM7982886	source name:Whole blood\|tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Burn\|geo loc name:missing\|collection date:missing	Burned Larval Zebrafish 48 hours post burn	FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix	Whole blood	Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.	tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Burn	GSM7982886	GSM7982886: Burned Larval Zebrafish 48 hours post burn; Danio rerio; RNA Seq	GSM7982886 r1	GSM7982886	1	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP479046	loader:fastq load.py	Burn-48hpb_S5_L002_R1_001.fastq.gz Burn-48hpb_S5_L002_R2_001.fastq.gz	fastq fastq	20022973425.0	171136525.0	GSM7982886 r2	0:28 1:89	A:5709681181;C:4208386174;G:4307510275;T:5796282368;N:1113427	28	89			5709681181	4208386174	4307510275	5796282368	1113427	SRX22969963	SRS19936063	SRA1772557	University of Wisconsin-Madison	University of Wisconsin-Madison	2	0.00547	0.9154	0.00202	0.1955	0.99283	0.79423	0.39307	0.53427	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2023-12-19	Multi-stage	Multi-stage	Blood	Hematopoietic System
29177	29177	SRR27292306	SRX22969962	SRS19936064	SRP479046	PRJNA1054617	Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish	GSE250610	Transcriptome Analysis	Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…	pubmed:38922186	Burned Larval Zebrafish 24 hours post burn	GSM7982885	source name:Whole blood\|tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Burn\|geo loc name:missing\|collection date:missing	Burned Larval Zebrafish 24 hours post burn	FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix	Whole blood	Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.	tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Burn	GSM7982885	GSM7982885: Burned Larval Zebrafish 24 hours post burn; Danio rerio; RNA Seq	GSM7982885 r1	GSM7982885	1	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP479046	loader:fastq load.py	Burn-24hpb_S2_L001_R1_001.fastq.gz Burn-24hpb_S2_L001_R2_001.fastq.gz	fastq fastq	9782870058.0	83614274.0	GSM7982885 r1	0:28 1:89	A:2744737668;C:2140848416;G:2249400157;T:2645170677;N:2713140	28	89			2744737668	2140848416	2249400157	2645170677	2713140	SRX22969962	SRS19936064	SRA1772557	University of Wisconsin-Madison	University of Wisconsin-Madison	2	0.00752	0.92059	0.00244	0.16143	0.98944	0.82929	0.44176	0.54525	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2023-12-19	Multi-stage	Multi-stage	Blood	Hematopoietic System
29178	29178	SRR27292307	SRX22969962	SRS19936064	SRP479046	PRJNA1054617	Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish	GSE250610	Transcriptome Analysis	Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…	pubmed:38922186	Burned Larval Zebrafish 24 hours post burn	GSM7982885	source name:Whole blood\|tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Burn\|geo loc name:missing\|collection date:missing	Burned Larval Zebrafish 24 hours post burn	FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix	Whole blood	Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.	tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Burn	GSM7982885	GSM7982885: Burned Larval Zebrafish 24 hours post burn; Danio rerio; RNA Seq	GSM7982885 r1	GSM7982885	1	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP479046	loader:fastq load.py	Burn-24hpb_S2_L002_R2_001.fastq.gz Burn-24hpb_S2_L002_R1_001.fastq.gz	fastq fastq	9861989202.0	84290506.0	GSM7982885 r2	0:28 1:89	A:2769268861;C:2158644227;G:2263475493;T:2669311436;N:1289185	28	89			2769268861	2158644227	2263475493	2669311436	1289185	SRX22969962	SRS19936064	SRA1772557	University of Wisconsin-Madison	University of Wisconsin-Madison	2	0.0076	0.9197	0.00232	0.16162	0.98995	0.82852	0.43786	0.55256	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2023-12-19	Multi-stage	Multi-stage	Blood	Hematopoietic System
29179	29179	SRR27292308	SRX22969961	SRS19936062	SRP479046	PRJNA1054617	Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish	GSE250610	Transcriptome Analysis	Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…	pubmed:38922186	Burned Larval Zebrafish 6 hours post burn	GSM7982884	source name:Whole blood\|tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Burn\|geo loc name:missing\|collection date:missing	Burned Larval Zebrafish 6 hours post burn	FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix	Whole blood	Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.	tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Burn	GSM7982884	GSM7982884: Burned Larval Zebrafish 6 hours post burn; Danio rerio; RNA Seq	GSM7982884 r1	GSM7982884	1	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP479046	loader:fastq load.py	Burn-6hpb_S7_L001_R1_001.fastq.gz Burn-6hpb_S7_L001_R2_001.fastq.gz	fastq fastq	12475938384.0	106631952.0	GSM7982884 r1	0:28 1:89	A:3401989108;C:2878275107;G:3114945415;T:3078525361;N:2203393	28	89			3401989108	2878275107	3114945415	3078525361	2203393	SRX22969961	SRS19936062	SRA1772557	University of Wisconsin-Madison	University of Wisconsin-Madison	2	0.01053	0.89396	0.00429	0.18315	0.99458	0.85756	0.34876	0.58728	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2023-12-19	Multi-stage	Multi-stage	Blood	Hematopoietic System
29180	29180	SRR27292309	SRX22969961	SRS19936062	SRP479046	PRJNA1054617	Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish	GSE250610	Transcriptome Analysis	Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…	pubmed:38922186	Burned Larval Zebrafish 6 hours post burn	GSM7982884	source name:Whole blood\|tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Burn\|geo loc name:missing\|collection date:missing	Burned Larval Zebrafish 6 hours post burn	FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix	Whole blood	Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.	tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Burn	GSM7982884	GSM7982884: Burned Larval Zebrafish 6 hours post burn; Danio rerio; RNA Seq	GSM7982884 r1	GSM7982884	1	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP479046	loader:fastq load.py	Burn-6hpb_S7_L002_R1_001.fastq.gz Burn-6hpb_S7_L002_R2_001.fastq.gz	fastq fastq	11874083247.0	101487891.0	GSM7982884 r2	0:28 1:89	A:3243501055;C:2735412615;G:2958387721;T:2936117380;N:664476	28	89			3243501055	2735412615	2958387721	2936117380	664476	SRX22969961	SRS19936062	SRA1772557	University of Wisconsin-Madison	University of Wisconsin-Madison	2	0.01063	0.89389	0.00439	0.18047	0.99403	0.85878	0.36393	0.54831	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2023-12-19	Multi-stage	Multi-stage	Blood	Hematopoietic System
29181	29181	SRR27292310	SRX22969960	SRS19936061	SRP479046	PRJNA1054617	Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish	GSE250610	Transcriptome Analysis	Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…	pubmed:38922186	Unwounded Larval Zebrafish 5 dpf	GSM7982883	source name:Whole blood\|tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Unwounded\|geo loc name:missing\|collection date:missing	Unwounded Larval Zebrafish 5 dpf	FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix	Whole blood	Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.	tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Unwounded	GSM7982883	GSM7982883: Unwounded Larval Zebrafish 5 dpf Danio rerio; RNA Seq	GSM7982883 r1	GSM7982883	1	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP479046	loader:fastq load.py	WT-5dpf_S6_L001_R2_001.fastq.gz WT-5dpf_S6_L001_R1_001.fastq.gz	fastq fastq	31813158312.0	271907336.0	GSM7982883 r1	0:28 1:89	A:8991313503;C:6911976524;G:7105775004;T:8798521232;N:5572049	28	89			8991313503	6911976524	7105775004	8798521232	5572049	SRX22969960	SRS19936061	SRA1772557	University of Wisconsin-Madison	University of Wisconsin-Madison	2	0.00661	0.92343	0.00245	0.19293	0.99255	0.81379	0.35935	0.54818	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2023-12-19	Multi-stage	Multi-stage	Blood	Hematopoietic System
29182	29182	SRR27292311	SRX22969960	SRS19936061	SRP479046	PRJNA1054617	Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish	GSE250610	Transcriptome Analysis	Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…	pubmed:38922186	Unwounded Larval Zebrafish 5 dpf	GSM7982883	source name:Whole blood\|tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Unwounded\|geo loc name:missing\|collection date:missing	Unwounded Larval Zebrafish 5 dpf	FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix	Whole blood	Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.	tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Unwounded	GSM7982883	GSM7982883: Unwounded Larval Zebrafish 5 dpf Danio rerio; RNA Seq	GSM7982883 r1	GSM7982883	1	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP479046	loader:fastq load.py	WT-5dpf_S6_L002_R1_001.fastq.gz WT-5dpf_S6_L002_R2_001.fastq.gz	fastq fastq	30524386113.0	260892189.0	GSM7982883 r2	0:28 1:89	A:8637605077;C:6625244702;G:6807369409;T:8452468968;N:1697957	28	89			8637605077	6625244702	6807369409	8452468968	1697957	SRX22969960	SRS19936061	SRA1772557	University of Wisconsin-Madison	University of Wisconsin-Madison	2	0.00648	0.92418	0.00233	0.19549	0.99241	0.81444	0.37733	0.54674	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2023-12-19	Multi-stage	Multi-stage	Blood	Hematopoietic System
29183	29183	SRR27292312	SRX22969959	SRS19936060	SRP479046	PRJNA1054617	Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish	GSE250610	Transcriptome Analysis	Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…	pubmed:38922186	Unwounded Larval Zebrafish 4 dpf	GSM7982882	source name:Whole blood\|tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Unwounded\|geo loc name:missing\|collection date:missing	Unwounded Larval Zebrafish 4 dpf	FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix	Whole blood	Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.	tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Unwounded	GSM7982882	GSM7982882: Unwounded Larval Zebrafish 4 dpf Danio rerio; RNA Seq	GSM7982882 r1	GSM7982882	1	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP479046	loader:fastq load.py	WT-4dpf_S1_L001_R1_001.fastq.gz WT-4dpf_S1_L001_R2_001.fastq.gz	fastq fastq	12682286721.0	108395613.0	GSM7982882 r1	0:28 1:89	A:3575375325;C:2777398557;G:2900088646;T:3425909511;N:3514682	28	89			3575375325	2777398557	2900088646	3425909511	3514682	SRX22969959	SRS19936060	SRA1772557	University of Wisconsin-Madison	University of Wisconsin-Madison	2	0.00505	0.92112	0.00185	0.16865	0.99257	0.8258	0.38216	0.5512	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2023-12-19	Multi-stage	Multi-stage	Blood	Hematopoietic System
29184	29184	SRR27292313	SRX22969959	SRS19936060	SRP479046	PRJNA1054617	Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish	GSE250610	Transcriptome Analysis	Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…	pubmed:38922186	Unwounded Larval Zebrafish 4 dpf	GSM7982882	source name:Whole blood\|tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Unwounded\|geo loc name:missing\|collection date:missing	Unwounded Larval Zebrafish 4 dpf	FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix	Whole blood	Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.	tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Unwounded	GSM7982882	GSM7982882: Unwounded Larval Zebrafish 4 dpf Danio rerio; RNA Seq	GSM7982882 r1	GSM7982882	1	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP479046	loader:fastq load.py	WT-4dpf_S1_L002_R2_001.fastq.gz WT-4dpf_S1_L002_R1_001.fastq.gz	fastq fastq	12832453413.0	109679089.0	GSM7982882 r2	0:28 1:89	A:3620789787;C:2810897812;G:2929508681;T:3469577031;N:1680102	28	89			3620789787	2810897812	2929508681	3469577031	1680102	SRX22969959	SRS19936060	SRA1772557	University of Wisconsin-Madison	University of Wisconsin-Madison	2	0.0052	0.92355	0.00192	0.16775	0.99263	0.8253	0.37089	0.55115	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2023-12-19	Multi-stage	Multi-stage	Blood	Hematopoietic System
29185	29185	SRR27292314	SRX22969958	SRS19936059	SRP479046	PRJNA1054617	Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish	GSE250610	Transcriptome Analysis	Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…	pubmed:38922186	Unwounded Larval Zebrafish 3 dpf	GSM7982881	source name:Whole blood\|tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Unwounded\|geo loc name:missing\|collection date:missing	Unwounded Larval Zebrafish 3 dpf	FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix	Whole blood	Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.	tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Unwounded	GSM7982881	GSM7982881: Unwounded Larval Zebrafish 3 dpf Danio rerio; RNA Seq	GSM7982881 r1	GSM7982881	1	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP479046	loader:fastq load.py	WT-3dpf_S4_L001_R1_001.fastq.gz WT-3dpf_S4_L001_R2_001.fastq.gz	fastq fastq	7586138430.0	64838790.0	GSM7982881 r1	0:28 1:89	A:2101749534;C:1692875352;G:1784872358;T:2005308370;N:1332816	28	89			2101749534	1692875352	1784872358	2005308370	1332816	SRX22969958	SRS19936059	SRA1772557	University of Wisconsin-Madison	University of Wisconsin-Madison	2	0.00976	0.92096	0.00368	0.18077	0.99356	0.83875	0.3661	0.59073	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2023-12-19	Multi-stage	Multi-stage	Blood	Hematopoietic System
29186	29186	SRR27292315	SRX22969958	SRS19936059	SRP479046	PRJNA1054617	Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish	GSE250610	Transcriptome Analysis	Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…	pubmed:38922186	Unwounded Larval Zebrafish 3 dpf	GSM7982881	source name:Whole blood\|tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Unwounded\|geo loc name:missing\|collection date:missing	Unwounded Larval Zebrafish 3 dpf	FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix	Whole blood	Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer.	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator.	tissue:Whole blood\|cell type:Macrophage\|cell type:Neutrophil\|genotype:WT\|treatment:Unwounded	GSM7982881	GSM7982881: Unwounded Larval Zebrafish 3 dpf Danio rerio; RNA Seq	GSM7982881 r1	GSM7982881	1	Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP479046	loader:fastq load.py	WT-3dpf_S4_L002_R1_001.fastq.gz WT-3dpf_S4_L002_R2_001.fastq.gz	fastq fastq	7258692168.0	62040104.0	GSM7982881 r2	0:28 1:89	A:2013529524;C:1617959197;G:1704796898;T:1922004726;N:401823	28	89			2013529524	1617959197	1704796898	1922004726	401823	SRX22969958	SRS19936059	SRA1772557	University of Wisconsin-Madison	University of Wisconsin-Madison	2	0.00949	0.92207	0.00359	0.18081	0.99375	0.83751	0.37347	0.55889	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2023-12-19	Multi-stage	Multi-stage	Blood	Hematopoietic System
30018	30018	SRR27988043	SRX23641260	SRS20476222	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		hamp / 36 hpf blood	zebrafish hamp / 36 hpf blood replicate 3	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:36 hpf\|dev stage:36 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:blood\|genotype:hamp knockdown\|sample type:tissue sample\|treatment:replicate 3\|BioSampleModel:Model organism or animal									RNA seq hamp / 36 hpf blood replicate 3	B 6	B 6	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		KO-3_R2_001.fastq.gz KO-3_R1_001.fastq.gz	fastq fastq	8752665900.0	29175553.0	KO 3 R1 001.fastq.gz	0:150 1:150	A:2204170575;C:2174083961;G:2224694970;T:2149603712;N:112682	150	150			2204170575	2174083961	2224694970	2149603712	112682	SRX23641260	SRS20476222	SRA1803422	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.91553	0.91645	0.01276	0.01288	0.85884	0.85839	0.35101	0.40996	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-02-16	Pharyngula	Embryo	Blood	Hematopoietic System
30019	30019	SRR27988044	SRX23641259	SRS20476221	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		hamp / 36 hpf blood	zebrafish hamp / 36 hpf blood replicate 2	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:36 hpf\|dev stage:36 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:blood\|genotype:hamp knockdown\|sample type:tissue sample\|treatment:replicate 2\|BioSampleModel:Model organism or animal									RNA seq hamp / 36 hpf blood replicate 2	B 5	B 5	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		KO-2_R1_001.fastq.gz KO-2_R2_001.fastq.gz	fastq fastq	8060498700.0	26868329.0	KO 2 R1 001.fastq.gz	0:150 1:150	A:2045797336;C:1985847523;G:2035528018;T:1993222840;N:102983	150	150			2045797336	1985847523	2035528018	1993222840	102983	SRX23641259	SRS20476221	SRA1803422	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.9213	0.92027	0.0167	0.01676	0.8242	0.82475	0.41081	0.41111	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-02-16	Pharyngula	Embryo	Blood	Hematopoietic System
30020	30020	SRR27988045	SRX23641258	SRS20476220	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		hamp / 36 hpf blood	zebrafish hamp / 36 hpf blood replicate 1	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:36 hpf\|dev stage:36 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:blood\|genotype:hamp knockdown\|sample type:tissue sample\|treatment:replicate 1\|BioSampleModel:Model organism or animal									RNA seq hamp / 36 hpf blood replicate 1	B 4	B 4	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		KO-1_R1_001.fastq.gz KO-1_R2_001.fastq.gz	fastq fastq	8707637700.0	29025459.0	KO 1 R1 001.fastq.gz	0:150 1:150	A:2222026435;C:2133480283;G:2182087972;T:2169932447;N:110563	150	150			2222026435	2133480283	2182087972	2169932447	110563	SRX23641258	SRS20476220	SRA1803422	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.91531	0.91359	0.02185	0.0221	0.81213	0.8128	0.37868	0.42351	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-02-16	Pharyngula	Embryo	Blood	Hematopoietic System
30021	30021	SRR27988046	SRX23641257	SRS20476219	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		wild type 36 hpf blood	zebrafish wild type 36 hpf blood replicate 3	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:36 hpf\|dev stage:36 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:blood\|genotype:wild type\|sample type:tissue sample\|treatment:replicate 3\|BioSampleModel:Model organism or animal									RNA seq wild type 36 hpf blood replicate 3	B 3	B 3	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		WT-3_R1_001.fastq.gz WT-3_R2_001.fastq.gz	fastq fastq	8829371400.0	29431238.0	WT 3 R1 001.fastq.gz	0:150 1:150	A:2278837675;C:2141723937;G:2193442375;T:2215253519;N:113894	150	150			2278837675	2141723937	2193442375	2215253519	113894	SRX23641257	SRS20476219	SRA1803422	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.90531	0.9043	0.03015	0.03017	0.8101	0.8112	0.43085	0.43002	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-02-16	Pharyngula	Embryo	Blood	Hematopoietic System
30022	30022	SRR27988047	SRX23641256	SRS20476218	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		wild type 36 hpf blood	zebrafish wild type 36 hpf blood replicate 2	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:36 hpf\|dev stage:36 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:blood\|genotype:wild type\|sample type:tissue sample\|treatment:replicate 2\|BioSampleModel:Model organism or animal									RNA seq wild type 36 hpf blood replicate 2	B 2	B 2	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		WT-2_R1_001.fastq.gz WT-2_R2_001.fastq.gz	fastq fastq	7365643800.0	24552146.0	WT 2 R1 001.fastq.gz	0:150 1:150	A:1867985067;C:1819016430;G:1870006707;T:1808540769;N:94827	150	150			1867985067	1819016430	1870006707	1808540769	94827	SRX23641256	SRS20476218	SRA1803422	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.90612	0.90536	0.01714	0.01746	0.88109	0.88156	0.32469	0.39232	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-02-16	Pharyngula	Embryo	Blood	Hematopoietic System
30023	30023	SRR27988048	SRX23641255	SRS20476217	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.		wild type 36 hpf blood	zebrafish wild type 36 hpf blood replicate 1	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:36 hpf\|dev stage:36 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:blood\|genotype:wild type\|sample type:tissue sample\|treatment:replicate 1\|BioSampleModel:Model organism or animal									RNA seq wild type 36 hpf blood replicate 1	B 1	B 1	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		WT-1_R1_001.fastq.gz WT-1_R2_001.fastq.gz	fastq fastq	8631863400.0	28772878.0	WT 1 R1 001.fastq.gz	0:150 1:150	A:2186212554;C:2135990723;G:2179142081;T:2130408485;N:109557	150	150			2186212554	2135990723	2179142081	2130408485	109557	SRX23641255	SRS20476217	SRA1803422	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.90461	0.90281	0.01388	0.01365	0.83871	0.83895	0.36511	0.41074	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-02-16	Pharyngula	Embryo	Blood	Hematopoietic System
31522	31522	SRR28418937	SRX24023264	SRS20817617	SRP497230	PRJNA1090848	Reprogramming of 3D genome structure underlying HSPC development in zebrafish [RNA seq]	GSE262188	Transcriptome Analysis	Development of hematopoietic stem and progenitor cells HSPC is a multi staged complex process that conserved between zebrafish and mammals; however the mechanism underlying HSPC development is not fully understood. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision its dynamic and role in HSPC development is poorly investigated. Here we performed chromatin structure and multi omics dissection across different stages of HSPC developmental trajectory in zebrafish. Chromatin organization of zebrafish HSPC resemble mammalian cells with similar hierarchical structure and characteristics. We revealed the multi scale reorganization of 3D genome and its influence on transcriptional regulation and transition of cell function during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably PU.1 was identified as a potential factor mediating formation of promoter involved loops and regulating gene expression as well as HSPC function. Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factor involved in HSPC chromatin interactions which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision. Overall design: To comprehensively dissect 3D genome rearrangement and its relation to transcriptional changes of zebrafish HSPC we get RNA seq results from adult sample. Then conjoint analysis of RNA seq with other datas can reveal the function of transcriptional factors such as PU.1 .	pubmed:38886858	HPSC rep3 RNA seq 3month	GSM8159257	source name:hematopoietic stem cell\|tissue:hematopoietic stem cell\|cell line:TgCD41:GFP gata1:dsRed\|cell type:hematopoietic stem cell\|genotype:CD41+gata1 \|time:3month\|treatment:flow cytometry\|geo loc name:missing\|collection date:missing	HPSC rep3 RNA seq 3month	The library is evaluated by FastQC. Readswith mean quality score less than orequal to 30 are removed. Raw reads were trimmed and removed for adapter sequences by fatspv.0.23.2 withpaired end default parameters. Extremely short fragment with length less than or equal to 30bp were also removed. post filtering high quality reads were aligned to GRCz10 zebrafish genome using HISAT2 with default parameters. FeatureCounts wasused to quantify gene expression and obtain reads count. Fold changes in gene transcription levels were estimated using DESeq2.Enrichment analysis of gene function was performed in the Metascape platform. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample	hematopoietic stem cell		Briefly ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U RNase inhibitor 10 U dNTP mix 10 mM each SS III first strand buffer 1× DTT 5 mM betaine 1 M MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina		tissue:hematopoietic stem cell\|cell line:TgCD41:GFP gata1:dsRed\|cell type:hematopoietic stem cell\|genotype:CD41+gata1 \|time:3month\|treatment:flow cytometry	GSM8159257	GSM8159257: HPSC rep3 RNA seq 3month; Danio rerio; RNA Seq	GSM8159257 r1	GSM8159257	1	Briefly ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U RNase inhibitor 10 U dNTP mix 10 mM each SS III first strand buffer 1× DTT 5 mM betaine 1 M MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP497230	loader:fastq load.py	RNA-seq_Adult_HPSC_rep3_R1.fq.gz RNA-seq_Adult_HPSC_rep3_R2.fq.gz	fastq fastq	11621758500.0	38739195.0	GSM8159257 r1	0:150 1:150	A:3144084931;C:2632272493;G:2693165513;T:3151802925;N:432638	150	150			3144084931	2632272493	2693165513	3151802925	432638	SRX24023264	SRS20817617	SRA1831889	South China University of Technology	South China University of Technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-03-21	Adult	Adult	Blood	Hematopoietic System
31523	31523	SRR28418938	SRX24023263	SRS20817616	SRP497230	PRJNA1090848	Reprogramming of 3D genome structure underlying HSPC development in zebrafish [RNA seq]	GSE262188	Transcriptome Analysis	Development of hematopoietic stem and progenitor cells HSPC is a multi staged complex process that conserved between zebrafish and mammals; however the mechanism underlying HSPC development is not fully understood. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision its dynamic and role in HSPC development is poorly investigated. Here we performed chromatin structure and multi omics dissection across different stages of HSPC developmental trajectory in zebrafish. Chromatin organization of zebrafish HSPC resemble mammalian cells with similar hierarchical structure and characteristics. We revealed the multi scale reorganization of 3D genome and its influence on transcriptional regulation and transition of cell function during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably PU.1 was identified as a potential factor mediating formation of promoter involved loops and regulating gene expression as well as HSPC function. Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factor involved in HSPC chromatin interactions which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision. Overall design: To comprehensively dissect 3D genome rearrangement and its relation to transcriptional changes of zebrafish HSPC we get RNA seq results from adult sample. Then conjoint analysis of RNA seq with other datas can reveal the function of transcriptional factors such as PU.1 .	pubmed:38886858	HPSC rep2 RNA seq 3month	GSM8159256	source name:hematopoietic stem cell\|tissue:hematopoietic stem cell\|cell line:TgCD41:GFP gata1:dsRed\|cell type:hematopoietic stem cell\|genotype:CD41+gata1 \|time:3month\|treatment:flow cytometry\|geo loc name:missing\|collection date:missing	HPSC rep2 RNA seq 3month	The library is evaluated by FastQC. Readswith mean quality score less than orequal to 30 are removed. Raw reads were trimmed and removed for adapter sequences by fatspv.0.23.2 withpaired end default parameters. Extremely short fragment with length less than or equal to 30bp were also removed. post filtering high quality reads were aligned to GRCz10 zebrafish genome using HISAT2 with default parameters. FeatureCounts wasused to quantify gene expression and obtain reads count. Fold changes in gene transcription levels were estimated using DESeq2.Enrichment analysis of gene function was performed in the Metascape platform. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample	hematopoietic stem cell		Briefly ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U RNase inhibitor 10 U dNTP mix 10 mM each SS III first strand buffer 1× DTT 5 mM betaine 1 M MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina		tissue:hematopoietic stem cell\|cell line:TgCD41:GFP gata1:dsRed\|cell type:hematopoietic stem cell\|genotype:CD41+gata1 \|time:3month\|treatment:flow cytometry	GSM8159256	GSM8159256: HPSC rep2 RNA seq 3month; Danio rerio; RNA Seq	GSM8159256 r1	GSM8159256	1	Briefly ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U RNase inhibitor 10 U dNTP mix 10 mM each SS III first strand buffer 1× DTT 5 mM betaine 1 M MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP497230	loader:fastq load.py	RNA-seq_Adult_HPSC_rep2_R1.fq.gz RNA-seq_Adult_HPSC_rep2_R2.fq.gz	fastq fastq	9951217200.0	33170724.0	GSM8159256 r1	0:150 1:150	A:2755384814;C:2209586340;G:2237522365;T:2748523249;N:200432	150	150			2755384814	2209586340	2237522365	2748523249	200432	SRX24023263	SRS20817616	SRA1831889	South China University of Technology	South China University of Technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-03-21	Adult	Adult	Blood	Hematopoietic System
31524	31524	SRR28418939	SRX24023262	SRS20817615	SRP497230	PRJNA1090848	Reprogramming of 3D genome structure underlying HSPC development in zebrafish [RNA seq]	GSE262188	Transcriptome Analysis	Development of hematopoietic stem and progenitor cells HSPC is a multi staged complex process that conserved between zebrafish and mammals; however the mechanism underlying HSPC development is not fully understood. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision its dynamic and role in HSPC development is poorly investigated. Here we performed chromatin structure and multi omics dissection across different stages of HSPC developmental trajectory in zebrafish. Chromatin organization of zebrafish HSPC resemble mammalian cells with similar hierarchical structure and characteristics. We revealed the multi scale reorganization of 3D genome and its influence on transcriptional regulation and transition of cell function during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably PU.1 was identified as a potential factor mediating formation of promoter involved loops and regulating gene expression as well as HSPC function. Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factor involved in HSPC chromatin interactions which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision. Overall design: To comprehensively dissect 3D genome rearrangement and its relation to transcriptional changes of zebrafish HSPC we get RNA seq results from adult sample. Then conjoint analysis of RNA seq with other datas can reveal the function of transcriptional factors such as PU.1 .	pubmed:38886858	HPSC rep1 RNA seq 3month	GSM8159255	source name:hematopoietic stem cell\|tissue:hematopoietic stem cell\|cell line:TgCD41:GFP gata1:dsRed\|cell type:hematopoietic stem cell\|genotype:CD41+gata1 \|time:3month\|treatment:flow cytometry\|geo loc name:missing\|collection date:missing	HPSC rep1 RNA seq 3month	The library is evaluated by FastQC. Readswith mean quality score less than orequal to 30 are removed. Raw reads were trimmed and removed for adapter sequences by fatspv.0.23.2 withpaired end default parameters. Extremely short fragment with length less than or equal to 30bp were also removed. post filtering high quality reads were aligned to GRCz10 zebrafish genome using HISAT2 with default parameters. FeatureCounts wasused to quantify gene expression and obtain reads count. Fold changes in gene transcription levels were estimated using DESeq2.Enrichment analysis of gene function was performed in the Metascape platform. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample	hematopoietic stem cell		Briefly ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U RNase inhibitor 10 U dNTP mix 10 mM each SS III first strand buffer 1× DTT 5 mM betaine 1 M MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina		tissue:hematopoietic stem cell\|cell line:TgCD41:GFP gata1:dsRed\|cell type:hematopoietic stem cell\|genotype:CD41+gata1 \|time:3month\|treatment:flow cytometry	GSM8159255	GSM8159255: HPSC rep1 RNA seq 3month; Danio rerio; RNA Seq	GSM8159255 r1	GSM8159255	1	Briefly ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U RNase inhibitor 10 U dNTP mix 10 mM each SS III first strand buffer 1× DTT 5 mM betaine 1 M MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP497230	loader:fastq load.py	RNA-seq_Adult_HPSC_rep1_R1.fq.gz RNA-seq_Adult_HPSC_rep1_R2.fq.gz	fastq fastq	11096617200.0	36988724.0	GSM8159255 r1	0:150 1:150	A:3071303610;C:2460399138;G:2510824334;T:3053621175;N:468943	150	150			3071303610	2460399138	2510824334	3053621175	468943	SRX24023262	SRS20817615	SRA1831889	South China University of Technology	South China University of Technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-03-21	Adult	Adult	Blood	Hematopoietic System
33075	33075	SRR29654109	SRX25158199	SRS21848821	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3	GSM8369980	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100	GSM8369980	GSM8369980: Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3; Danio rerio; RNA Seq	GSM8369980 r1	GSM8369980	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_AMD_-016_cbc.fastq.gz	fastq	347162880.0	5786048.0	GSM8369980 r1	0:60	A:122562825;C:62219285;G:75539895;T:86775172;N:65703	60				122562825	62219285	75539895	86775172	65703	SRX25158199	SRS21848821	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33076	33076	SRR29654110	SRX25158199	SRS21848821	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3	GSM8369980	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100	GSM8369980	GSM8369980: Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3; Danio rerio; RNA Seq	GSM8369980 r1	GSM8369980	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_AMD_-016_cbc.fastq.gz	fastq	340954260.0	5682571.0	GSM8369980 r2	0:60	A:120149623;C:60854408;G:75192893;T:84703966;N:53370	60				120149623	60854408	75192893	84703966	53370	SRX25158199	SRS21848821	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33077	33077	SRR29654111	SRX25158199	SRS21848821	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3	GSM8369980	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100	GSM8369980	GSM8369980: Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3; Danio rerio; RNA Seq	GSM8369980 r1	GSM8369980	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_AMD_-016_cbc.fastq.gz	fastq	351749160.0	5862486.0	GSM8369980 r3	0:60	A:124352905;C:63078724;G:76291828;T:87988386;N:37317	60				124352905	63078724	76291828	87988386	37317	SRX25158199	SRS21848821	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33078	33078	SRR29654112	SRX25158199	SRS21848821	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3	GSM8369980	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100	GSM8369980	GSM8369980: Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3; Danio rerio; RNA Seq	GSM8369980 r1	GSM8369980	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_AMD_-016_cbc.fastq.gz	fastq	345225720.0	5753762.0	GSM8369980 r4	0:60	A:121803902;C:61651407;G:75900430;T:85843789;N:26192	60				121803902	61651407	75900430	85843789	26192	SRX25158199	SRS21848821	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33079	33079	SRR29654113	SRX25158198	SRS21848820	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2	GSM8369979	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100	GSM8369979	GSM8369979: Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2; Danio rerio; RNA Seq	GSM8369979 r1	GSM8369979	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_AMD_-015_cbc.fastq.gz	fastq	159497640.0	2658294.0	GSM8369979 r1	0:60	A:55569742;C:28678683;G:33264744;T:41953354;N:31117	60				55569742	28678683	33264744	41953354	31117	SRX25158198	SRS21848820	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33080	33080	SRR29654114	SRX25158198	SRS21848820	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2	GSM8369979	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100	GSM8369979	GSM8369979: Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2; Danio rerio; RNA Seq	GSM8369979 r1	GSM8369979	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_AMD_-015_cbc.fastq.gz	fastq	156549240.0	2609154.0	GSM8369979 r2	0:60	A:54428858;C:28027289;G:33149650;T:40918247;N:25196	60				54428858	28027289	33149650	40918247	25196	SRX25158198	SRS21848820	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33081	33081	SRR29654115	SRX25158198	SRS21848820	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2	GSM8369979	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100	GSM8369979	GSM8369979: Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2; Danio rerio; RNA Seq	GSM8369979 r1	GSM8369979	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_AMD_-015_cbc.fastq.gz	fastq	161735280.0	2695588.0	GSM8369979 r3	0:60	A:56425187;C:29084972;G:33637112;T:42570603;N:17406	60				56425187	29084972	33637112	42570603	17406	SRX25158198	SRS21848820	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33082	33082	SRR29654116	SRX25158198	SRS21848820	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2	GSM8369979	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100	GSM8369979	GSM8369979: Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2; Danio rerio; RNA Seq	GSM8369979 r1	GSM8369979	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_AMD_-015_cbc.fastq.gz	fastq	158621520.0	2643692.0	GSM8369979 r4	0:60	A:55213721;C:28430013;G:33462307;T:41503213;N:12266	60				55213721	28430013	33462307	41503213	12266	SRX25158198	SRS21848820	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33083	33083	SRR29654117	SRX25158197	SRS21848819	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1	GSM8369978	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100	GSM8369978	GSM8369978: Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1; Danio rerio; RNA Seq	GSM8369978 r1	GSM8369978	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_AMD_-011_cbc.fastq.gz	fastq	44363040.0	739384.0	GSM8369978 r1	0:60	A:17756825;C:7540147;G:9311367;T:9746444;N:8257	60				17756825	7540147	9311367	9746444	8257	SRX25158197	SRS21848819	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33084	33084	SRR29654118	SRX25158197	SRS21848819	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1	GSM8369978	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100	GSM8369978	GSM8369978: Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1; Danio rerio; RNA Seq	GSM8369978 r1	GSM8369978	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_AMD_-011_cbc.fastq.gz	fastq	43450800.0	724180.0	GSM8369978 r2	0:60	A:17376442;C:7355139;G:9244019;T:9468455;N:6745	60				17376442	7355139	9244019	9468455	6745	SRX25158197	SRS21848819	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33085	33085	SRR29654119	SRX25158197	SRS21848819	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1	GSM8369978	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100	GSM8369978	GSM8369978: Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1; Danio rerio; RNA Seq	GSM8369978 r1	GSM8369978	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_AMD_-011_cbc.fastq.gz	fastq	44795880.0	746598.0	GSM8369978 r3	0:60	A:17988707;C:7600964;G:9362568;T:9839285;N:4356	60				17988707	7600964	9362568	9839285	4356	SRX25158197	SRS21848819	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33086	33086	SRR29654120	SRX25158197	SRS21848819	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1	GSM8369978	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100	GSM8369978	GSM8369978: Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1; Danio rerio; RNA Seq	GSM8369978 r1	GSM8369978	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_AMD_-011_cbc.fastq.gz	fastq	44060940.0	734349.0	GSM8369978 r4	0:60	A:17608648;C:7492643;G:9327676;T:9628642;N:3331	60				17608648	7492643	9327676	9628642	3331	SRX25158197	SRS21848819	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33087	33087	SRR29654121	SRX25158196	SRS21848818	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ uninjured AMD3100 biol rep 3	GSM8369977	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured AMD3100 biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100	GSM8369977	GSM8369977: Neutrophils mpx+ uninjured AMD3100 biol rep 3; Danio rerio; RNA Seq	GSM8369977 r1	GSM8369977	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_AMD_-014_cbc.fastq.gz	fastq	115048140.0	1917469.0	GSM8369977 r1	0:60	A:41373215;C:21759509;G:21832537;T:30061744;N:21135	60				41373215	21759509	21832537	30061744	21135	SRX25158196	SRS21848818	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33088	33088	SRR29654122	SRX25158196	SRS21848818	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ uninjured AMD3100 biol rep 3	GSM8369977	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured AMD3100 biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100	GSM8369977	GSM8369977: Neutrophils mpx+ uninjured AMD3100 biol rep 3; Danio rerio; RNA Seq	GSM8369977 r1	GSM8369977	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_AMD_-014_cbc.fastq.gz	fastq	112845060.0	1880751.0	GSM8369977 r2	0:60	A:40482360;C:21287713;G:21750928;T:29306465;N:17594	60				40482360	21287713	21750928	29306465	17594	SRX25158196	SRS21848818	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33089	33089	SRR29654123	SRX25158196	SRS21848818	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ uninjured AMD3100 biol rep 3	GSM8369977	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured AMD3100 biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100	GSM8369977	GSM8369977: Neutrophils mpx+ uninjured AMD3100 biol rep 3; Danio rerio; RNA Seq	GSM8369977 r1	GSM8369977	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_AMD_-014_cbc.fastq.gz	fastq	116696580.0	1944943.0	GSM8369977 r3	0:60	A:42022776;C:22106040;G:22075778;T:30479513;N:12473	60				42022776	22106040	22075778	30479513	12473	SRX25158196	SRS21848818	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33090	33090	SRR29654124	SRX25158196	SRS21848818	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ uninjured AMD3100 biol rep 3	GSM8369977	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured AMD3100 biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100	GSM8369977	GSM8369977: Neutrophils mpx+ uninjured AMD3100 biol rep 3; Danio rerio; RNA Seq	GSM8369977 r1	GSM8369977	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_AMD_-014_cbc.fastq.gz	fastq	114334980.0	1905583.0	GSM8369977 r4	0:60	A:41132105;C:21578779;G:21934073;T:29681512;N:8511	60				41132105	21578779	21934073	29681512	8511	SRX25158196	SRS21848818	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33091	33091	SRR29654125	SRX25158195	SRS21848817	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ uninjured AMD3100 biol rep 2	GSM8369976	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured AMD3100 biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100	GSM8369976	GSM8369976: Neutrophils mpx+ uninjured AMD3100 biol rep 2; Danio rerio; RNA Seq	GSM8369976 r1	GSM8369976	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_AMD_-013_cbc.fastq.gz	fastq	354085380.0	5901423.0	GSM8369976 r1	0:60	A:124800871;C:65627966;G:72434440;T:91152029;N:70074	60				124800871	65627966	72434440	91152029	70074	SRX25158195	SRS21848817	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33092	33092	SRR29654126	SRX25158195	SRS21848817	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ uninjured AMD3100 biol rep 2	GSM8369976	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured AMD3100 biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100	GSM8369976	GSM8369976: Neutrophils mpx+ uninjured AMD3100 biol rep 2; Danio rerio; RNA Seq	GSM8369976 r1	GSM8369976	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_AMD_-013_cbc.fastq.gz	fastq	347250360.0	5787506.0	GSM8369976 r2	0:60	A:122147080;C:64042522;G:72135325;T:88869927;N:55506	60				122147080	64042522	72135325	88869927	55506	SRX25158195	SRS21848817	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33093	33093	SRR29654127	SRX25158195	SRS21848817	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ uninjured AMD3100 biol rep 2	GSM8369976	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured AMD3100 biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100	GSM8369976	GSM8369976: Neutrophils mpx+ uninjured AMD3100 biol rep 2; Danio rerio; RNA Seq	GSM8369976 r1	GSM8369976	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_AMD_-013_cbc.fastq.gz	fastq	358862580.0	5981043.0	GSM8369976 r3	0:60	A:126636264;C:66527902;G:73214426;T:92445348;N:38640	60				126636264	66527902	73214426	92445348	38640	SRX25158195	SRS21848817	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33094	33094	SRR29654128	SRX25158195	SRS21848817	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ uninjured AMD3100 biol rep 2	GSM8369976	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured AMD3100 biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100	GSM8369976	GSM8369976: Neutrophils mpx+ uninjured AMD3100 biol rep 2; Danio rerio; RNA Seq	GSM8369976 r1	GSM8369976	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_AMD_-013_cbc.fastq.gz	fastq	351843120.0	5864052.0	GSM8369976 r4	0:60	A:123921807;C:64956560;G:72828989;T:90107944;N:27820	60				123921807	64956560	72828989	90107944	27820	SRX25158195	SRS21848817	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33095	33095	SRR29654129	SRX25158194	SRS21848816	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ uninjured AMD3100 biol rep 1	GSM8369975	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured AMD3100 biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100	GSM8369975	GSM8369975: Neutrophils mpx+ uninjured AMD3100 biol rep 1; Danio rerio; RNA Seq	GSM8369975 r1	GSM8369975	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_AMD_-010_cbc.fastq.gz	fastq	100732380.0	1678873.0	GSM8369975 r1	0:60	A:37215898;C:18610797;G:18111317;T:26774380;N:19988	60				37215898	18610797	18111317	26774380	19988	SRX25158194	SRS21848816	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33096	33096	SRR29654130	SRX25158194	SRS21848816	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ uninjured AMD3100 biol rep 1	GSM8369975	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured AMD3100 biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100	GSM8369975	GSM8369975: Neutrophils mpx+ uninjured AMD3100 biol rep 1; Danio rerio; RNA Seq	GSM8369975 r1	GSM8369975	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_AMD_-010_cbc.fastq.gz	fastq	98830860.0	1647181.0	GSM8369975 r2	0:60	A:36388012;C:18195984;G:18122717;T:26108692;N:15455	60				36388012	18195984	18122717	26108692	15455	SRX25158194	SRS21848816	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33097	33097	SRR29654131	SRX25158194	SRS21848816	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ uninjured AMD3100 biol rep 1	GSM8369975	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured AMD3100 biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100	GSM8369975	GSM8369975: Neutrophils mpx+ uninjured AMD3100 biol rep 1; Danio rerio; RNA Seq	GSM8369975 r1	GSM8369975	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_AMD_-010_cbc.fastq.gz	fastq	102277560.0	1704626.0	GSM8369975 r3	0:60	A:37811843;C:18928051;G:18347174;T:27179477;N:11015	60				37811843	18928051	18347174	27179477	11015	SRX25158194	SRS21848816	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33098	33098	SRR29654132	SRX25158194	SRS21848816	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ uninjured AMD3100 biol rep 1	GSM8369975	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured AMD3100 biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100	GSM8369975	GSM8369975: Neutrophils mpx+ uninjured AMD3100 biol rep 1; Danio rerio; RNA Seq	GSM8369975 r1	GSM8369975	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_AMD_-010_cbc.fastq.gz	fastq	100371840.0	1672864.0	GSM8369975 r4	0:60	A:37032383;C:18500721;G:18308236;T:26522753;N:7747	60				37032383	18500721	18308236	26522753	7747	SRX25158194	SRS21848816	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33099	33099	SRR29654133	SRX25158193	SRS21848815	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3	GSM8369974	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO	GSM8369974	GSM8369974: Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3; Danio rerio; RNA Seq	GSM8369974 r1	GSM8369974	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_DMSO_-008_cbc.fastq.gz	fastq	161717520.0	2695292.0	GSM8369974 r1	0:60	A:58227035;C:29120167;G:33153372;T:41186362;N:30584	60				58227035	29120167	33153372	41186362	30584	SRX25158193	SRS21848815	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33100	33100	SRR29654134	SRX25158193	SRS21848815	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3	GSM8369974	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO	GSM8369974	GSM8369974: Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3; Danio rerio; RNA Seq	GSM8369974 r1	GSM8369974	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_DMSO_-008_cbc.fastq.gz	fastq	158810460.0	2646841.0	GSM8369974 r2	0:60	A:57059029;C:28475827;G:33090143;T:40160441;N:25020	60				57059029	28475827	33090143	40160441	25020	SRX25158193	SRS21848815	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33101	33101	SRR29654135	SRX25158193	SRS21848815	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3	GSM8369974	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO	GSM8369974	GSM8369974: Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3; Danio rerio; RNA Seq	GSM8369974 r1	GSM8369974	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_DMSO_-008_cbc.fastq.gz	fastq	164136600.0	2735610.0	GSM8369974 r3	0:60	A:59164760;C:29564845;G:33567677;T:41822336;N:16982	60				59164760	29564845	33567677	41822336	16982	SRX25158193	SRS21848815	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33102	33102	SRR29654136	SRX25158193	SRS21848815	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3	GSM8369974	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO	GSM8369974	GSM8369974: Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3; Danio rerio; RNA Seq	GSM8369974 r1	GSM8369974	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_DMSO_-008_cbc.fastq.gz	fastq	160939740.0	2682329.0	GSM8369974 r4	0:60	A:57905646;C:28872433;G:33402085;T:40746636;N:12940	60				57905646	28872433	33402085	40746636	12940	SRX25158193	SRS21848815	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33103	33103	SRR29654137	SRX25158192	SRS21848814	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2	GSM8369973	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO	GSM8369973	GSM8369973: Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2; Danio rerio; RNA Seq	GSM8369973 r1	GSM8369973	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_DMSO_-005_cbc.fastq.gz	fastq	294896760.0	4914946.0	GSM8369973 r1	0:60	A:113302890;C:53832811;G:54274745;T:73429183;N:57131	60				113302890	53832811	54274745	73429183	57131	SRX25158192	SRS21848814	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33104	33104	SRR29654138	SRX25158192	SRS21848814	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2	GSM8369973	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO	GSM8369973	GSM8369973: Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2; Danio rerio; RNA Seq	GSM8369973 r1	GSM8369973	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_DMSO_-005_cbc.fastq.gz	fastq	289658820.0	4827647.0	GSM8369973 r2	0:60	A:111138289;C:52646716;G:54190664;T:71637241;N:45910	60				111138289	52646716	54190664	71637241	45910	SRX25158192	SRS21848814	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33105	33105	SRR29654139	SRX25158192	SRS21848814	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2	GSM8369973	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO	GSM8369973	GSM8369973: Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2; Danio rerio; RNA Seq	GSM8369973 r1	GSM8369973	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_DMSO_-005_cbc.fastq.gz	fastq	299290800.0	4988180.0	GSM8369973 r3	0:60	A:115247052;C:54662821;G:54854607;T:74494831;N:31489	60				115247052	54662821	54854607	74494831	31489	SRX25158192	SRS21848814	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33106	33106	SRR29654140	SRX25158192	SRS21848814	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2	GSM8369973	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO	GSM8369973	GSM8369973: Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2; Danio rerio; RNA Seq	GSM8369973 r1	GSM8369973	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_DMSO_-005_cbc.fastq.gz	fastq	294091920.0	4901532.0	GSM8369973 r4	0:60	A:113032051;C:53520496;G:54754695;T:72762244;N:22434	60				113032051	53520496	54754695	72762244	22434	SRX25158192	SRS21848814	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33107	33107	SRR29654141	SRX25158191	SRS21848813	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1	GSM8369972	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO	GSM8369972	GSM8369972: Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1; Danio rerio; RNA Seq	GSM8369972 r1	GSM8369972	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_DMSO_-004_cbc.fastq.gz	fastq	79542600.0	1325710.0	GSM8369972 r1	0:60	A:29052800;C:15106261;G:15344010;T:20023888;N:15641	60				29052800	15106261	15344010	20023888	15641	SRX25158191	SRS21848813	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33108	33108	SRR29654142	SRX25158191	SRS21848813	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1	GSM8369972	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO	GSM8369972	GSM8369972: Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1; Danio rerio; RNA Seq	GSM8369972 r1	GSM8369972	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_DMSO_-004_cbc.fastq.gz	fastq	78150840.0	1302514.0	GSM8369972 r2	0:60	A:28490299;C:14795977;G:15298357;T:19554765;N:11442	60				28490299	14795977	15298357	19554765	11442	SRX25158191	SRS21848813	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33109	33109	SRR29654143	SRX25158191	SRS21848813	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1	GSM8369972	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO	GSM8369972	GSM8369972: Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1; Danio rerio; RNA Seq	GSM8369972 r1	GSM8369972	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_DMSO_-004_cbc.fastq.gz	fastq	80719140.0	1345319.0	GSM8369972 r3	0:60	A:29548150;C:15350378;G:15486892;T:20325654;N:8066	60				29548150	15350378	15486892	20325654	8066	SRX25158191	SRS21848813	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33110	33110	SRR29654144	SRX25158191	SRS21848813	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1	GSM8369972	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO	GSM8369972	GSM8369972: Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1; Danio rerio; RNA Seq	GSM8369972 r1	GSM8369972	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_DMSO_-004_cbc.fastq.gz	fastq	79070760.0	1317846.0	GSM8369972 r4	0:60	A:28874779;C:14986197;G:15407453;T:19795922;N:6409	60				28874779	14986197	15407453	19795922	6409	SRX25158191	SRS21848813	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33111	33111	SRR29654145	SRX25158190	SRS21848812	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ uninjured DMSO biol rep 3	GSM8369971	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured DMSO biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO	GSM8369971	GSM8369971: Neutrophils mpx+ uninjured DMSO biol rep 3; Danio rerio; RNA Seq	GSM8369971 r1	GSM8369971	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_DMSO_-009_cbc.fastq.gz	fastq	182391600.0	3039860.0	GSM8369971 r1	0:60	A:65842196;C:33929963;G:37226765;T:45358269;N:34407	60				65842196	33929963	37226765	45358269	34407	SRX25158190	SRS21848812	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33112	33112	SRR29654146	SRX25158190	SRS21848812	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ uninjured DMSO biol rep 3	GSM8369971	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured DMSO biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO	GSM8369971	GSM8369971: Neutrophils mpx+ uninjured DMSO biol rep 3; Danio rerio; RNA Seq	GSM8369971 r1	GSM8369971	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_DMSO_-009_cbc.fastq.gz	fastq	179081640.0	2984694.0	GSM8369971 r2	0:60	A:64544585;C:33163305;G:37078756;T:44266486;N:28508	60				64544585	33163305	37078756	44266486	28508	SRX25158190	SRS21848812	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33113	33113	SRR29654147	SRX25158190	SRS21848812	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ uninjured DMSO biol rep 3	GSM8369971	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured DMSO biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO	GSM8369971	GSM8369971: Neutrophils mpx+ uninjured DMSO biol rep 3; Danio rerio; RNA Seq	GSM8369971 r1	GSM8369971	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_DMSO_-009_cbc.fastq.gz	fastq	185068740.0	3084479.0	GSM8369971 r3	0:60	A:66919946;C:34450944;G:37652300;T:46025841;N:19709	60				66919946	34450944	37652300	46025841	19709	SRX25158190	SRS21848812	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33114	33114	SRR29654148	SRX25158190	SRS21848812	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ uninjured DMSO biol rep 3	GSM8369971	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured DMSO biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO	GSM8369971	GSM8369971: Neutrophils mpx+ uninjured DMSO biol rep 3; Danio rerio; RNA Seq	GSM8369971 r1	GSM8369971	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_DMSO_-009_cbc.fastq.gz	fastq	181507740.0	3025129.0	GSM8369971 r4	0:60	A:65513514;C:33675079;G:37432606;T:44872485;N:14056	60				65513514	33675079	37432606	44872485	14056	SRX25158190	SRS21848812	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33115	33115	SRR29654149	SRX25158189	SRS21848811	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ uninjured DMSO biol rep 2	GSM8369970	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured DMSO biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO	GSM8369970	GSM8369970: Neutrophils mpx+ uninjured DMSO biol rep 2; Danio rerio; RNA Seq	GSM8369970 r1	GSM8369970	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_DMSO_-006_cbc.fastq.gz	fastq	45794760.0	763246.0	GSM8369970 r1	0:60	A:16928569;C:8492491;G:9006326;T:11358172;N:9202	60				16928569	8492491	9006326	11358172	9202	SRX25158189	SRS21848811	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33116	33116	SRR29654150	SRX25158189	SRS21848811	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ uninjured DMSO biol rep 2	GSM8369970	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured DMSO biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO	GSM8369970	GSM8369970: Neutrophils mpx+ uninjured DMSO biol rep 2; Danio rerio; RNA Seq	GSM8369970 r1	GSM8369970	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_DMSO_-006_cbc.fastq.gz	fastq	45009960.0	750166.0	GSM8369970 r2	0:60	A:16608407;C:8309766;G:8990622;T:11094414;N:6751	60				16608407	8309766	8990622	11094414	6751	SRX25158189	SRS21848811	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33117	33117	SRR29654151	SRX25158189	SRS21848811	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ uninjured DMSO biol rep 2	GSM8369970	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured DMSO biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO	GSM8369970	GSM8369970: Neutrophils mpx+ uninjured DMSO biol rep 2; Danio rerio; RNA Seq	GSM8369970 r1	GSM8369970	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_DMSO_-006_cbc.fastq.gz	fastq	46565880.0	776098.0	GSM8369970 r3	0:60	A:17217451;C:8640544;G:9146095;T:11557146;N:4644	60				17217451	8640544	9146095	11557146	4644	SRX25158189	SRS21848811	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33118	33118	SRR29654152	SRX25158189	SRS21848811	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ uninjured DMSO biol rep 2	GSM8369970	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured DMSO biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO	GSM8369970	GSM8369970: Neutrophils mpx+ uninjured DMSO biol rep 2; Danio rerio; RNA Seq	GSM8369970 r1	GSM8369970	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_DMSO_-006_cbc.fastq.gz	fastq	45624660.0	760411.0	GSM8369970 r4	0:60	A:16852187;C:8431444;G:9090234;T:11246907;N:3888	60				16852187	8431444	9090234	11246907	3888	SRX25158189	SRS21848811	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33119	33119	SRR29654153	SRX25158188	SRS21848810	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ uninjured DMSO biol rep 1	GSM8369969	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured DMSO biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO	GSM8369969	GSM8369969: Neutrophils mpx+ uninjured DMSO biol rep 1; Danio rerio; RNA Seq	GSM8369969 r1	GSM8369969	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_DMSO_-003_cbc.fastq.gz	fastq	55867380.0	931123.0	GSM8369969 r1	0:60	A:20680346;C:10254613;G:10895370;T:14026951;N:10100	60				20680346	10254613	10895370	14026951	10100	SRX25158188	SRS21848810	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33120	33120	SRR29654154	SRX25158188	SRS21848810	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ uninjured DMSO biol rep 1	GSM8369969	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured DMSO biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO	GSM8369969	GSM8369969: Neutrophils mpx+ uninjured DMSO biol rep 1; Danio rerio; RNA Seq	GSM8369969 r1	GSM8369969	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_DMSO_-003_cbc.fastq.gz	fastq	54889080.0	914818.0	GSM8369969 r2	0:60	A:20264110;C:10026239;G:10861715;T:13728039;N:8977	60				20264110	10026239	10861715	13728039	8977	SRX25158188	SRS21848810	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33121	33121	SRR29654155	SRX25158188	SRS21848810	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ uninjured DMSO biol rep 1	GSM8369969	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured DMSO biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO	GSM8369969	GSM8369969: Neutrophils mpx+ uninjured DMSO biol rep 1; Danio rerio; RNA Seq	GSM8369969 r1	GSM8369969	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_DMSO_-003_cbc.fastq.gz	fastq	56764440.0	946074.0	GSM8369969 r3	0:60	A:21036899;C:10416984;G:11027830;T:14275499;N:7228	60				21036899	10416984	11027830	14275499	7228	SRX25158188	SRS21848810	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33122	33122	SRR29654156	SRX25158188	SRS21848810	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal	pubmed:38925414	Neutrophils mpx+ uninjured DMSO biol rep 1	GSM8369969	tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured DMSO biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO	GSM8369969	GSM8369969: Neutrophils mpx+ uninjured DMSO biol rep 1; Danio rerio; RNA Seq	GSM8369969 r1	GSM8369969	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033		IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_DMSO_-003_cbc.fastq.gz	fastq	55531080.0	925518.0	GSM8369969 r4	0:60	A:20538193;C:10150017;G:10949669;T:13888674;N:4527	60				20538193	10150017	10949669	13888674	4527	SRX25158188	SRS21848810	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
35485	35485	SRR32834031	SRX28117245	SRS24473023	SRP572644	PRJNA1241156	Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish	GSE292726	Transcriptome Analysis	Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.		mCherry cells rag1 crispant R848 treated	GSM8864273	tissue:Hematopoietic & Immune Cells\|cell type:Hematopoietic & Immune Cells\|genotype:rag1 mosaic mutant\|treatment:Resiquimod R848 treated\|geo loc name:missing\|collection date:missing	mCherry cells rag1 crispant R848 treated	For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix	Hematopoietic & Immune Cells	The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	Larvae were maintained in standard conditions at 28C	cell type:Hematopoietic & Immune Cells\|genotype:rag1 mosaic mutant\|treatment:Resiquimod R848 treated	GSM8864273	GSM8864273: mCherry cells rag1 crispant R848 treated; Danio rerio; RNA Seq	GSM8864273 r1	GSM8864273	1	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP572644	loader:fastq load.py\|options: readTypes=TBTT read1PairFiles=Rag1 crispant with R848 S64 L005 R1 001.fastq.gz read2PairFiles=Rag1 crispant with R848 S64 L005 R2 001.fastq.gz read3PairFiles=Rag1 crispant with R848 S64 L005 I1 001.fastq.gz read4PairFiles=Rag1 crispant with R848 S64 L005 I2 001.fastq.gz	Rag1_crispant_with_R848_S64_L005_I1_001.fastq.gz Rag1_crispant_with_R848_S64_L005_I2_001.fastq.gz Rag1_crispant_with_R848_S64_L005_R1_001.fastq.gz Rag1_crispant_with_R848_S64_L005_R2_001.fastq.gz	fastq fastq fastq fastq	51690121264.0	371871376.0	GSM8864273 r1	0:28 1:91 2:10 3:10	A:9268291738;C:7690563124;G:8398909329;T:8480309041;N:2221984	28	91	10	10	9268291738	7690563124	8398909329	8480309041	2221984	SRX28117245	SRS24473023	SRA2098862	Albert Einstein College of Medicine	Albert Einstein College of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-03-24	Larval	Larval	Blood	Hematopoietic System
35486	35486	SRR32834032	SRX28117244	SRS24473025	SRP572644	PRJNA1241156	Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish	GSE292726	Transcriptome Analysis	Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.		mCherry cells slc24a5 crispant R848 treated	GSM8864272	tissue:Hematopoietic & Immune Cells\|cell type:Hematopoietic & Immune Cells\|genotype:slc24a5 mosaic mutant\|treatment:Resiquimod R848 treated\|geo loc name:missing\|collection date:missing	mCherry cells slc24a5 crispant R848 treated	For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix	Hematopoietic & Immune Cells	The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	Larvae were maintained in standard conditions at 28C	cell type:Hematopoietic & Immune Cells\|genotype:slc24a5 mosaic mutant\|treatment:Resiquimod R848 treated	GSM8864272	GSM8864272: mCherry cells slc24a5 crispant R848 treated; Danio rerio; RNA Seq	GSM8864272 r1	GSM8864272	1	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP572644	loader:fastq load.py\|options: readTypes=TBTT read1PairFiles=slc24a5 crispant with R848 S62 L005 R1 001.fastq.gz read2PairFiles=slc24a5 crispant with R848 S62 L005 R2 001.fastq.gz read3PairFiles=slc24a5 crispant with R848 S62 L005 I1 001.fastq.gz read4PairFiles=slc24a5 crispant with R848 S62 L005 I2 001.fastq.gz	slc24a5_crispant_with_R848_S62_L005_I1_001.fastq.gz slc24a5_crispant_with_R848_S62_L005_I2_001.fastq.gz slc24a5_crispant_with_R848_S62_L005_R1_001.fastq.gz slc24a5_crispant_with_R848_S62_L005_R2_001.fastq.gz	fastq fastq fastq fastq	67359016638.0	484597242.0	GSM8864272 r1	0:28 1:91 2:10 3:10	A:12101967291;C:10017190111;G:10977547337;T:10998758556;N:2885727	28	91	10	10	12101967291	10017190111	10977547337	10998758556	2885727	SRX28117244	SRS24473025	SRA2098862	Albert Einstein College of Medicine	Albert Einstein College of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-03-24	Larval	Larval	Blood	Hematopoietic System
35487	35487	SRR32834033	SRX28117243	SRS24473024	SRP572644	PRJNA1241156	Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish	GSE292726	Transcriptome Analysis	Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.		mCherry cells rag1 crispant	GSM8864271	tissue:Hematopoietic & Immune Cells\|cell type:Hematopoietic & Immune Cells\|genotype:rag1 mosaic mutant\|geo loc name:missing\|collection date:missing	mCherry cells rag1 crispant	For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix	Hematopoietic & Immune Cells	The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	Larvae were maintained in standard conditions at 28C	cell type:Hematopoietic & Immune Cells\|genotype:rag1 mosaic mutant	GSM8864271	GSM8864271: mCherry cells rag1 crispant; Danio rerio; RNA Seq	GSM8864271 r1	GSM8864271	1	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP572644	loader:fastq load.py\|options: readTypes=TBTT read1PairFiles=Rag1 crispant S63 L005 R1 001.fastq.gz read2PairFiles=Rag1 crispant S63 L005 R2 001.fastq.gz read3PairFiles=Rag1 crispant S63 L005 I1 001.fastq.gz read4PairFiles=Rag1 crispant S63 L005 I2 001.fastq.gz	Rag1_crispant_S63_L005_I1_001.fastq.gz Rag1_crispant_S63_L005_I2_001.fastq.gz Rag1_crispant_S63_L005_R1_001.fastq.gz Rag1_crispant_S63_L005_R2_001.fastq.gz	fastq fastq fastq fastq	40550115550.0	291727450.0	GSM8864271 r1	0:28 1:91 2:10 3:10	A:7262987235;C:6078752458;G:6639990009;T:6563701562;N:1766686	28	91	10	10	7262987235	6078752458	6639990009	6563701562	1766686	SRX28117243	SRS24473024	SRA2098862	Albert Einstein College of Medicine	Albert Einstein College of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-03-24	Larval	Larval	Blood	Hematopoietic System
35488	35488	SRR32834034	SRX28117242	SRS24473022	SRP572644	PRJNA1241156	Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish	GSE292726	Transcriptome Analysis	Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.		mCherry cells slc24a5 crispant	GSM8864270	tissue:Hematopoietic & Immune Cells\|cell type:Hematopoietic & Immune Cells\|genotype:slc24a5 mosaic mutant\|geo loc name:missing\|collection date:missing	mCherry cells slc24a5 crispant	For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix	Hematopoietic & Immune Cells	The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	Larvae were maintained in standard conditions at 28C	cell type:Hematopoietic & Immune Cells\|genotype:slc24a5 mosaic mutant	GSM8864270	GSM8864270: mCherry cells slc24a5 crispant; Danio rerio; RNA Seq	GSM8864270 r1	GSM8864270	1	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP572644	loader:fastq load.py\|options: readTypes=TBTT read1PairFiles=slc24a5 crispant S61 L005 R1 001.fastq.gz read2PairFiles=slc24a5 crispant S61 L005 R2 001.fastq.gz read3PairFiles=slc24a5 crispant S61 L005 I1 001.fastq.gz read4PairFiles=slc24a5 crispant S61 L005 I2 001.fastq.gz	slc24a5_crispant_S61_L005_I1_001.fastq.gz slc24a5_crispant_S61_L005_I2_001.fastq.gz slc24a5_crispant_S61_L005_R1_001.fastq.gz slc24a5_crispant_S61_L005_R2_001.fastq.gz	fastq fastq fastq fastq	53500554564.0	384896076.0	GSM8864270 r1	0:28 1:91 2:10 3:10	A:9607899809;C:8061049626;G:8772491787;T:8581787300;N:2314394	28	91	10	10	9607899809	8061049626	8772491787	8581787300	2314394	SRX28117242	SRS24473022	SRA2098862	Albert Einstein College of Medicine	Albert Einstein College of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-03-24	Larval	Larval	Blood	Hematopoietic System
35489	35489	SRR32834035	SRX28117241	SRS24473017	SRP572644	PRJNA1241156	Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish	GSE292726	Transcriptome Analysis	Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.		mCherry cells runx1 homozygous mutants	GSM8864269	tissue:Hematopoietic & Immune Cells\|cell type:Hematopoietic & Immune Cells\|genotype:runx1 homozygous\|geo loc name:missing\|collection date:missing	mCherry cells runx1 homozygous mutants	For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix	Hematopoietic & Immune Cells	The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	Larvae were maintained in standard conditions at 28C	cell type:Hematopoietic & Immune Cells\|genotype:runx1 homozygous	GSM8864269	GSM8864269: mCherry cells runx1 homozygous mutants; Danio rerio; RNA Seq	GSM8864269 r1	GSM8864269	1	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP572644	loader:fastq load.py\|options: readTypes=TBTT read1PairFiles=Runx1 Homz Mutants earlyHSPC trace 6 dpf S2 L002 R1 001.fastq.gz read2PairFiles=Runx1 Homz Mutants earlyHSPC trace 6 dpf S2 L002 R2 001.fastq.gz read3PairFiles=Runx1 Homz Mutants earlyHSPC trace 6 dpf S2 L002 I1 001.fastq.gz read4PairFiles=Runx1 Homz Mutants earlyHSPC trace 6 dpf S2 L002 I2 001.fastq.gz	Runx1_Homz_Mutants_earlyHSPC_trace_6_dpf_S2_L002_I1_001.fastq.gz Runx1_Homz_Mutants_earlyHSPC_trace_6_dpf_S2_L002_I2_001.fastq.gz Runx1_Homz_Mutants_earlyHSPC_trace_6_dpf_S2_L002_R1_001.fastq.gz Runx1_Homz_Mutants_earlyHSPC_trace_6_dpf_S2_L002_R2_001.fastq.gz	fastq fastq fastq fastq	27845512960.0	87017228.0	GSM8864269 r1	0:150 1:150 2:10 3:10	A:4012440512;C:2615250336;G:3042659166;T:3381797139;N:437047	150	150	10	10	4012440512	2615250336	3042659166	3381797139	437047	SRX28117241	SRS24473017	SRA2098862	Albert Einstein College of Medicine	Albert Einstein College of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-03-24	Larval	Larval	Blood	Hematopoietic System
35490	35490	SRR32834036	SRX28117240	SRS24473018	SRP572644	PRJNA1241156	Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish	GSE292726	Transcriptome Analysis	Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.		mCherry cells sibling controls	GSM8864268	tissue:Hematopoietic & Immune Cells\|cell type:Hematopoietic & Immune Cells\|genotype:wild type or runx1 heterozygous\|geo loc name:missing\|collection date:missing	mCherry cells sibling controls	For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix	Hematopoietic & Immune Cells	The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	Larvae were maintained in standard conditions at 28C	cell type:Hematopoietic & Immune Cells\|genotype:wild type or runx1 heterozygous	GSM8864268	GSM8864268: mCherry cells sibling controls; Danio rerio; RNA Seq	GSM8864268 r1	GSM8864268	1	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP572644	loader:fastq load.py\|options: readTypes=TBTT read1PairFiles=Sibling Control earlyHSPC trace 6 dpf S1 L002 R1 001.fastq.gz read2PairFiles=Sibling Control earlyHSPC trace 6 dpf S1 L002 R2 001.fastq.gz read3PairFiles=Sibling Control earlyHSPC trace 6 dpf S1 L002 I1 001.fastq.gz read4PairFiles=Sibling Control earlyHSPC trace 6 dpf S1 L002 I2 001.fastq.gz	Sibling_Control_earlyHSPC_trace_6_dpf_S1_L002_I1_001.fastq.gz Sibling_Control_earlyHSPC_trace_6_dpf_S1_L002_I2_001.fastq.gz Sibling_Control_earlyHSPC_trace_6_dpf_S1_L002_R1_001.fastq.gz Sibling_Control_earlyHSPC_trace_6_dpf_S1_L002_R2_001.fastq.gz	fastq fastq fastq fastq	24953253760.0	77978918.0	GSM8864268 r1	0:150 1:150 2:10 3:10	A:3390875336;C:2571521800;G:2871954356;T:2862416982;N:69226	150	150	10	10	3390875336	2571521800	2871954356	2862416982	69226	SRX28117240	SRS24473018	SRA2098862	Albert Einstein College of Medicine	Albert Einstein College of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-03-24	Larval	Larval	Blood	Hematopoietic System
35491	35491	SRR32834037	SRX28117239	SRS24473015	SRP572644	PRJNA1241156	Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish	GSE292726	Transcriptome Analysis	Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.		mCherry cells late HSPCs 10 dpf	GSM8864267	tissue:Hematopoietic & Immune Cells\|cell type:Hematopoietic & Immune Cells\|geo loc name:missing\|collection date:missing	mCherry cells late HSPCs 10 dpf	For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix	Hematopoietic & Immune Cells	The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	Larvae were maintained in standard conditions at 28C	cell type:Hematopoietic & Immune Cells	GSM8864267	GSM8864267: mCherry cells late HSPCs 10 dpf; Danio rerio; RNA Seq	GSM8864267 r1	GSM8864267	1	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP572644	loader:fastq load.py\|options: readTypes=TBTT read1PairFiles=lateHSPC trace at 10dpf S1 L003 R1 001.fastq.gz read2PairFiles=lateHSPC trace at 10dpf S1 L003 R2 001.fastq.gz read3PairFiles=lateHSPC trace at 10dpf S1 L003 I1 001.fastq.gz read4PairFiles=lateHSPC trace at 10dpf S1 L003 I2 001.fastq.gz	lateHSPC_trace_at_10dpf_S1_L003_I1_001.fastq.gz lateHSPC_trace_at_10dpf_S1_L003_I2_001.fastq.gz lateHSPC_trace_at_10dpf_S1_L003_R1_001.fastq.gz lateHSPC_trace_at_10dpf_S1_L003_R2_001.fastq.gz	fastq fastq fastq fastq	49750537600.0	155470430.0	GSM8864267 r1	0:150 1:150 2:10 3:10	A:6695708919;C:5110107098;G:5648204020;T:5864962224;N:1582239	150	150	10	10	6695708919	5110107098	5648204020	5864962224	1582239	SRX28117239	SRS24473015	SRA2098862	Albert Einstein College of Medicine	Albert Einstein College of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-03-24	Larval	Larval	Blood	Hematopoietic System
35492	35492	SRR32834038	SRX28117239	SRS24473015	SRP572644	PRJNA1241156	Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish	GSE292726	Transcriptome Analysis	Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.		mCherry cells late HSPCs 10 dpf	GSM8864267	tissue:Hematopoietic & Immune Cells\|cell type:Hematopoietic & Immune Cells\|geo loc name:missing\|collection date:missing	mCherry cells late HSPCs 10 dpf	For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix	Hematopoietic & Immune Cells	The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	Larvae were maintained in standard conditions at 28C	cell type:Hematopoietic & Immune Cells	GSM8864267	GSM8864267: mCherry cells late HSPCs 10 dpf; Danio rerio; RNA Seq	GSM8864267 r1	GSM8864267	1	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP572644	loader:fastq load.py\|options: readTypes=TBTT read1PairFiles=lateHSPC trace at 10dpf S18 L002 R1 001.fastq.gz read2PairFiles=lateHSPC trace at 10dpf S18 L002 R2 001.fastq.gz read3PairFiles=lateHSPC trace at 10dpf S18 L002 I1 001.fastq.gz read4PairFiles=lateHSPC trace at 10dpf S18 L002 I2 001.fastq.gz	lateHSPC_trace_at_10dpf_S18_L002_I1_001.fastq.gz lateHSPC_trace_at_10dpf_S18_L002_I2_001.fastq.gz lateHSPC_trace_at_10dpf_S18_L002_R1_001.fastq.gz lateHSPC_trace_at_10dpf_S18_L002_R2_001.fastq.gz	fastq fastq fastq fastq	3818546250.0	27670625.0	GSM8864267 r2	0:28 1:90 2:10 3:10	A:716133237;C:554493684;G:608989896;T:610460128;N:279305	28	90	10	10	716133237	554493684	608989896	610460128	279305	SRX28117239	SRS24473015	SRA2098862	Albert Einstein College of Medicine	Albert Einstein College of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-03-24	Larval	Larval	Blood	Hematopoietic System
35493	35493	SRR32834039	SRX28117238	SRS24473019	SRP572644	PRJNA1241156	Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish	GSE292726	Transcriptome Analysis	Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.		mCherry cells late HSPCs 6 dpf	GSM8864266	tissue:Hematopoietic & Immune Cells\|cell type:Hematopoietic & Immune Cells\|geo loc name:missing\|collection date:missing	mCherry cells late HSPCs 6 dpf	For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix	Hematopoietic & Immune Cells	The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	Larvae were maintained in standard conditions at 28C	cell type:Hematopoietic & Immune Cells	GSM8864266	GSM8864266: mCherry cells late HSPCs 6 dpf; Danio rerio; RNA Seq	GSM8864266 r1	GSM8864266	1	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP572644	loader:fastq load.py\|options: readTypes=TBTT read1PairFiles=lateHSPC trace at 6dpf S17 L002 R1 001.fastq.gz read2PairFiles=lateHSPC trace at 6dpf S17 L002 R2 001.fastq.gz read3PairFiles=lateHSPC trace at 6dpf S17 L002 I1 001.fastq.gz read4PairFiles=lateHSPC trace at 6dpf S17 L002 I2 001.fastq.gz	lateHSPC_trace_at_6dpf_S17_L002_I1_001.fastq.gz lateHSPC_trace_at_6dpf_S17_L002_I2_001.fastq.gz lateHSPC_trace_at_6dpf_S17_L002_R1_001.fastq.gz lateHSPC_trace_at_6dpf_S17_L002_R2_001.fastq.gz	fastq fastq fastq fastq	12871712088.0	93273276.0	GSM8864266 r1	0:28 1:90 2:10 3:10	A:2421583617;C:1888963122;G:2078815965;T:2004213972;N:1018164	28	90	10	10	2421583617	1888963122	2078815965	2004213972	1018164	SRX28117238	SRS24473019	SRA2098862	Albert Einstein College of Medicine	Albert Einstein College of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-03-24	Larval	Larval	Blood	Hematopoietic System
35494	35494	SRR32834040	SRX28117237	SRS24473014	SRP572644	PRJNA1241156	Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish	GSE292726	Transcriptome Analysis	Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.		mCherry cells late HSPCs 4 dpf	GSM8864265	tissue:Hematopoietic & Immune Cells\|cell type:Hematopoietic & Immune Cells\|geo loc name:missing\|collection date:missing	mCherry cells late HSPCs 4 dpf	For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix	Hematopoietic & Immune Cells	The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	Larvae were maintained in standard conditions at 28C	cell type:Hematopoietic & Immune Cells	GSM8864265	GSM8864265: mCherry cells late HSPCs 4 dpf; Danio rerio; RNA Seq	GSM8864265 r1	GSM8864265	1	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP572644	loader:fastq load.py\|options: readTypes=TBTT read1PairFiles=lateHSPC trace at 4dpf S16 L002 R1 001.fastq.gz read2PairFiles=lateHSPC trace at 4dpf S16 L002 R2 001.fastq.gz read3PairFiles=lateHSPC trace at 4dpf S16 L002 I1 001.fastq.gz read4PairFiles=lateHSPC trace at 4dpf S16 L002 I2 001.fastq.gz	lateHSPC_trace_at_4dpf_S16_L002_I1_001.fastq.gz lateHSPC_trace_at_4dpf_S16_L002_I2_001.fastq.gz lateHSPC_trace_at_4dpf_S16_L002_R1_001.fastq.gz lateHSPC_trace_at_4dpf_S16_L002_R2_001.fastq.gz	fastq fastq fastq fastq	11138275734.0	80712143.0	GSM8864265 r1	0:28 1:90 2:10 3:10	A:2022661838;C:1679042427;G:1720706851;T:1840857883;N:823871	28	90	10	10	2022661838	1679042427	1720706851	1840857883	823871	SRX28117237	SRS24473014	SRA2098862	Albert Einstein College of Medicine	Albert Einstein College of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-03-24	Larval	Larval	Blood	Hematopoietic System
35495	35495	SRR32834041	SRX28117236	SRS24473016	SRP572644	PRJNA1241156	Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish	GSE292726	Transcriptome Analysis	Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.		mCherry cells mid HSPCs 10 dpf	GSM8864264	tissue:Hematopoietic & Immune Cells\|cell type:Hematopoietic & Immune Cells\|geo loc name:missing\|collection date:missing	mCherry cells mid HSPCs 10 dpf	For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix	Hematopoietic & Immune Cells	The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	Larvae were maintained in standard conditions at 28C	cell type:Hematopoietic & Immune Cells	GSM8864264	GSM8864264: mCherry cells mid HSPCs 10 dpf; Danio rerio; RNA Seq	GSM8864264 r1	GSM8864264	1	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP572644	loader:fastq load.py\|options: readTypes=TBTT read1PairFiles=midHSPC 10dpf S1 L001 R1 001.fastq.gz read2PairFiles=midHSPC 10dpf S1 L001 R2 001.fastq.gz read3PairFiles=midHSPC 10dpf S1 L001 I1 001.fastq.gz read4PairFiles=midHSPC 10dpf S1 L001 I2 001.fastq.gz	midHSPC_10dpf_S1_L001_I1_001.fastq.gz midHSPC_10dpf_S1_L001_I2_001.fastq.gz midHSPC_10dpf_S1_L001_R1_001.fastq.gz midHSPC_10dpf_S1_L001_R2_001.fastq.gz	fastq fastq fastq fastq	211217834240.0	660055732.0	GSM8864264 r1	0:150 1:150 2:10 3:10	A:28426769480;C:22300370613;G:24520861829;T:23758933345;N:1424533	150	150	10	10	28426769480	22300370613	24520861829	23758933345	1424533	SRX28117236	SRS24473016	SRA2098862	Albert Einstein College of Medicine	Albert Einstein College of Medicine												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-03-24	Larval	Larval	Blood	Hematopoietic System
35496	35496	SRR32834042	SRX28117235	SRS24473020	SRP572644	PRJNA1241156	Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish	GSE292726	Transcriptome Analysis	Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.		mCherry cells mid HSPCs 6 dpf	GSM8864263	tissue:Hematopoietic & Immune Cells\|cell type:Hematopoietic & Immune Cells\|geo loc name:missing\|collection date:missing	mCherry cells mid HSPCs 6 dpf	For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix	Hematopoietic & Immune Cells	The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	Larvae were maintained in standard conditions at 28C	cell type:Hematopoietic & Immune Cells	GSM8864263	GSM8864263: mCherry cells mid HSPCs 6 dpf; Danio rerio; RNA Seq	GSM8864263 r1	GSM8864263	1	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP572644	loader:fastq load.py\|options: readTypes=TBTT read1PairFiles=midHSPC 6dpf S1 L001 R1 001.fastq.gz read2PairFiles=midHSPC 6dpf S1 L001 R2 001.fastq.gz read3PairFiles=midHSPC 6dpf S1 L001 I1 001.fastq.gz read4PairFiles=midHSPC 6dpf S1 L001 I2 001.fastq.gz	midHSPC_6dpf_S1_L001_I1_001.fastq.gz midHSPC_6dpf_S1_L001_I2_001.fastq.gz midHSPC_6dpf_S1_L001_R1_001.fastq.gz midHSPC_6dpf_S1_L001_R2_001.fastq.gz	fastq fastq fastq fastq	241173414720.0	753666921.0	GSM8864263 r1												SRX28117235	SRS24473020	SRA2098862	Albert Einstein College of Medicine	Albert Einstein College of Medicine	1	0.94667		0.08748		0.83881		0.5015		150		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-03-24	Larval	Larval	Blood	Hematopoietic System
35497	35497	SRR32834043	SRX28117234	SRS24473021	SRP572644	PRJNA1241156	Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish	GSE292726	Transcriptome Analysis	Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.		mCherry cells mid HSPCs 3 dpf	GSM8864262	tissue:Hematopoietic & Immune Cells\|cell type:Hematopoietic & Immune Cells\|geo loc name:missing\|collection date:missing	mCherry cells mid HSPCs 3 dpf	For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix	Hematopoietic & Immune Cells	The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	Larvae were maintained in standard conditions at 28C	cell type:Hematopoietic & Immune Cells	GSM8864262	GSM8864262: mCherry cells mid HSPCs 3 dpf; Danio rerio; RNA Seq	GSM8864262 r1	GSM8864262	1	Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP572644	loader:fastq load.py\|options: readTypes=TBTT read1PairFiles=midHSPC 3dpf S6 L003 R1 001.fastq.gz read2PairFiles=midHSPC 3dpf S6 L003 R2 001.fastq.gz read3PairFiles=midHSPC 3dpf S6 L003 I1 001.fastq.gz read4PairFiles=midHSPC 3dpf S6 L003 I2 001.fastq.gz	midHSPC_3dpf_S6_L003_I1_001.fastq.gz midHSPC_3dpf_S6_L003_I2_001.fastq.gz midHSPC_3dpf_S6_L003_R1_001.fastq.gz midHSPC_3dpf_S6_L003_R2_001.fastq.gz	fastq fastq fastq fastq	71933359680.0	224791749.0	GSM8864262 r1	0:150 1:150 2:10 3:10	A:9519625855;C:6982221178;G:8366028895;T:7767873072;N:1083013350	150	150	10	10	9519625855	6982221178	8366028895	7767873072	1083013350	SRX28117234	SRS24473021	SRA2098862	Albert Einstein College of Medicine	Albert Einstein College of Medicine	1	0.78368		0.08584		0.82144		0.50936		150		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-03-24	Larval	Larval	Blood	Hematopoietic System

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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");;