metadata: run_metadata: 201 rows where experiment.library_layout = "SINGLE", experiment.library_source = "TRANSCRIPTOMIC" and tissue

201 rows where experiment.library_layout = "SINGLE", experiment.library_source = "TRANSCRIPTOMIC" 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.attributes	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.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	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
25304	25304	SRR25793376	SRX21515638	SRS18742880	SRP457465	PRJNA1010662	The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.	PRJNA1010662	Other	Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.		RNA seq Erythrocytes miR 144 adult	miR 144 adult	isolate:miR 144 mutant\|age:Adult\|collection date:N/A\|geo loc name:N/A\|sex:mixed\|tissue:Blood\|BioSampleModel:Model organism or animal									Quant seq Erythrocytes miR 144 mutant Danio rerio ADULT replicate 1	144 1 adult blood	144 1 adult blood	Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457465		DC-144AL1_S10.fastq	fastq	781435052.0	17368946.0	DC 144AL1 S10.fastq	0:44.99	A:207445570;C:148430622;G:177122903;T:245179579;N:3256378	44		207445570	148430622	177122903	245179579	3256378	SRX21515638	SRS18742880	SRA1701831	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.8759	0.28126	0.95051	0.47905	22	B	usable mapping rate	illumina	novaseq_era	3prime	poly_a	lexogen	bulk	unknown	unknown	United Kingdom	2023-08-30	Adult	Adult	Blood	Hematopoietic System
25305	25305	SRR25793377	SRX21515637	SRS18742882	SRP457465	PRJNA1010662	The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.	PRJNA1010662	Other	Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.		RNA seq Erythrocytes Wild type adult	WT adult	isolate:Wildtype\|age:Adult\|collection date:N/A\|geo loc name:N/A\|sex:mixed\|tissue:Blood\|BioSampleModel:Model organism or animal									Quant seq Erythrocytes Wild type Danio rerio ADULT replicate 3	WT3 adult blood	WT3 adult blood	Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457465		DC-WTA3_S6.fastq	fastq	601997398.0	17290043.0	DC WTA3 S6.fastq	0:34.82	A:136034449;C:142779447;G:177204517;T:134955264;N:11023721	34		136034449	142779447	177204517	134955264	11023721	SRX21515637	SRS18742882	SRA1701831	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.32909	0.08525	0.95288	0.60214	22	B	usable mapping rate	illumina	novaseq_era	3prime	poly_a	lexogen	bulk	unknown	unknown	United Kingdom	2023-08-30	Adult	Adult	Blood	Hematopoietic System
25306	25306	SRR25793378	SRX21515636	SRS18742882	SRP457465	PRJNA1010662	The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.	PRJNA1010662	Other	Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.		RNA seq Erythrocytes Wild type adult	WT adult	isolate:Wildtype\|age:Adult\|collection date:N/A\|geo loc name:N/A\|sex:mixed\|tissue:Blood\|BioSampleModel:Model organism or animal									Quant seq Erythrocytes Wild type Danio rerio ADULT replicate 2	WT2 adult blood	WT2 adult blood	Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457465		DC-WTA2_S5.fastq	fastq	669871903.0	17381581.0	DC WTA2 S5.fastq	0:38.54	A:169704437;C:140964096;G:160484620;T:189596855;N:9121895	38		169704437	140964096	160484620	189596855	9121895	SRX21515636	SRS18742882	SRA1701831	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.69865	0.19099	0.93432	0.47502	68	B	usable mapping rate	illumina	novaseq_era	3prime	poly_a	lexogen	bulk	unknown	unknown	United Kingdom	2023-08-30	Adult	Adult	Blood	Hematopoietic System
25307	25307	SRR25793379	SRX21515635	SRS18742882	SRP457465	PRJNA1010662	The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.	PRJNA1010662	Other	Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.		RNA seq Erythrocytes Wild type adult	WT adult	isolate:Wildtype\|age:Adult\|collection date:N/A\|geo loc name:N/A\|sex:mixed\|tissue:Blood\|BioSampleModel:Model organism or animal									Quant seq Erythrocytes Wild type Danio rerio ADULT replicate 1	WT1 adult blood	WT1 adult blood	Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457465		DC-WTA1_S4.fastq	fastq	824193699.0	17465379.0	DC WTA1 S4.fastq	0:47.19	A:209553199;C:169966117;G:194322860;T:244145525;N:6205998	47		209553199	169966117	194322860	244145525	6205998	SRX21515635	SRS18742882	SRA1701831	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.76241	0.25975	0.94619	0.50211	66	B	usable mapping rate	illumina	novaseq_era	3prime	poly_a	lexogen	bulk	unknown	unknown	United Kingdom	2023-08-30	Adult	Adult	Blood	Hematopoietic System
25308	25308	SRR25793380	SRX21515634	SRS18742881	SRP457465	PRJNA1010662	The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.	PRJNA1010662	Other	Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.		RNA seq Erythrocytes miR 144 embryo	miR 144 embryo	isolate:miR 144 mutant\|age:Embryo\|collection date:N/A\|geo loc name:N/A\|sex:mixed\|tissue:Blood\|BioSampleModel:Model organism or animal									Quant seq Erythrocytes miR 144 mutant Danio rerio 2 dpf replicate 3	144 3 embryo blood	144 3 embryo blood	Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457465		DC-144EL3_S18.fastq	fastq	687309797.0	17039739.0	DC 144EL3 S18.fastq	0:40.34	A:159186558;C:130452893;G:155820002;T:181676510;N:60173834	40		159186558	130452893	155820002	181676510	60173834	SRX21515634	SRS18742881	SRA1701831	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.52966	0.16941	0.97615	0.58418	61	B	usable mapping rate	illumina	novaseq_era	3prime	poly_a	lexogen	bulk	unknown	unknown	United Kingdom	2023-08-30	Hatching	Embryo	Blood	Hematopoietic System
25309	25309	SRR25793381	SRX21515633	SRS18742881	SRP457465	PRJNA1010662	The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.	PRJNA1010662	Other	Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.		RNA seq Erythrocytes miR 144 embryo	miR 144 embryo	isolate:miR 144 mutant\|age:Embryo\|collection date:N/A\|geo loc name:N/A\|sex:mixed\|tissue:Blood\|BioSampleModel:Model organism or animal									Quant seq Erythrocytes miR 144 mutant Danio rerio 2 dpf replicate 2	144 2 embryo blood	144 2 embryo blood	Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457465		DC-144EL2_S17.fastq	fastq	495318731.0	14459195.0	DC 144EL2 S17.fastq	0:34.26	A:110392869;C:106378418;G:128881687;T:107956679;N:41709078	34		110392869	106378418	128881687	107956679	41709078	SRX21515633	SRS18742881	SRA1701831	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.32147	0.04496	0.97569	0.58512	31	B	usable mapping rate	illumina	novaseq_era	3prime	poly_a	lexogen	bulk	unknown	unknown	United Kingdom	2023-08-30	Hatching	Embryo	Blood	Hematopoietic System
25310	25310	SRR25793382	SRX21515632	SRS18742881	SRP457465	PRJNA1010662	The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.	PRJNA1010662	Other	Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.		RNA seq Erythrocytes miR 144 embryo	miR 144 embryo	isolate:miR 144 mutant\|age:Embryo\|collection date:N/A\|geo loc name:N/A\|sex:mixed\|tissue:Blood\|BioSampleModel:Model organism or animal									Quant seq Erythrocytes miR 144 mutant Danio rerio 2 dpf replicate 1	144 1 embryo blood	144 1 embryo blood	Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457465		DC-144EL1_S16.fastq	fastq	974854100.0	20079553.0	DC 144EL1 S16.fastq	0:48.55	A:233861010;C:192987350;G:215192262;T:269960344;N:62853134	48		233861010	192987350	215192262	269960344	62853134	SRX21515632	SRS18742881	SRA1701831	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.77953	0.18084	0.90905	0.74157	75	B	usable mapping rate	illumina	novaseq_era	3prime	poly_a	lexogen	bulk	unknown	unknown	United Kingdom	2023-08-30	Hatching	Embryo	Blood	Hematopoietic System
25311	25311	SRR25793383	SRX21515631	SRS18742879	SRP457465	PRJNA1010662	The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.	PRJNA1010662	Other	Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.		RNA seq Erythrocytes Wild type embryo	WT embryo	isolate:Wildtype\|age:Embryo\|collection date:N/A\|geo loc name:N/A\|sex:mixed\|tissue:Blood\|BioSampleModel:Model organism or animal									Quant seq Erythrocytes Wild type Danio rerio 2 dpf replicate 3	WT3 embryo blood	WT3 embryo blood	Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457465		DC-WTE3_S15.fastq	fastq	657139116.0	15618072.0	DC WTE3 S15.fastq	0:42.08	A:154495614;C:122942896;G:147719345;T:179403193;N:52578068	42		154495614	122942896	147719345	179403193	52578068	SRX21515631	SRS18742879	SRA1701831	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.56358	0.19381	0.96757	0.6115	76	B	usable mapping rate	illumina	novaseq_era	3prime	poly_a	lexogen	bulk	unknown	unknown	United Kingdom	2023-08-30	Hatching	Embryo	Blood	Hematopoietic System
25312	25312	SRR25793384	SRX21515630	SRS18742880	SRP457465	PRJNA1010662	The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.	PRJNA1010662	Other	Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.		RNA seq Erythrocytes miR 144 adult	miR 144 adult	isolate:miR 144 mutant\|age:Adult\|collection date:N/A\|geo loc name:N/A\|sex:mixed\|tissue:Blood\|BioSampleModel:Model organism or animal									Quant seq Erythrocytes miR 144 mutant Danio rerio ADULT replicate 3	144 3 adult blood	144 3 adult blood	Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457465		DC-144AL3_S12.fastq	fastq	498938612.0	14861511.0	DC 144AL3 S12.fastq	0:33.57	A:137243823;C:96735877;G:109220779;T:152042235;N:3695898	33		137243823	96735877	109220779	152042235	3695898	SRX21515630	SRS18742880	SRA1701831	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.82213	0.16617	0.95053	0.46386	22	B	usable mapping rate	illumina	novaseq_era	3prime	poly_a	lexogen	bulk	unknown	unknown	United Kingdom	2023-08-30	Adult	Adult	Blood	Hematopoietic System
25313	25313	SRR25793385	SRX21515629	SRS18742880	SRP457465	PRJNA1010662	The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.	PRJNA1010662	Other	Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.		RNA seq Erythrocytes miR 144 adult	miR 144 adult	isolate:miR 144 mutant\|age:Adult\|collection date:N/A\|geo loc name:N/A\|sex:mixed\|tissue:Blood\|BioSampleModel:Model organism or animal									Quant seq Erythrocytes miR 144 mutant Danio rerio ADULT replicate 2	144 2 adult blood	144 2 adult blood	Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457465		DC-144AL2_S11.fastq	fastq	497890134.0	10636306.0	DC 144AL2 S11.fastq	0:46.81	A:134598214;C:94036725;G:109501897;T:158719603;N:1033695	46		134598214	94036725	109501897	158719603	1033695	SRX21515629	SRS18742880	SRA1701831	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.88496	0.29132	0.96002	0.53343	22	B	usable mapping rate	illumina	novaseq_era	3prime	poly_a	lexogen	bulk	unknown	unknown	United Kingdom	2023-08-30	Adult	Adult	Blood	Hematopoietic System
25314	25314	SRR25793386	SRX21515628	SRS18742879	SRP457465	PRJNA1010662	The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.	PRJNA1010662	Other	Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.		RNA seq Erythrocytes Wild type embryo	WT embryo	isolate:Wildtype\|age:Embryo\|collection date:N/A\|geo loc name:N/A\|sex:mixed\|tissue:Blood\|BioSampleModel:Model organism or animal									Quant seq Erythrocytes Wild type Danio rerio 2 dpf replicate 2	WT2 embryo blood	WT2 embryo blood	Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457465		DC-WTE2_S14.fastq	fastq	250958009.0	9755304.0	DC WTE2 S14.fastq	0:25.73	A:43225839;C:41823862;G:54150092;T:43159724;N:68598492	25		43225839	41823862	54150092	43159724	68598492	SRX21515628	SRS18742879	SRA1701831	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.34114	0.05466	0.96664	0.54625	47	B	usable mapping rate	illumina	novaseq_era	3prime	poly_a	lexogen	bulk	unknown	unknown	United Kingdom	2023-08-30	Hatching	Embryo	Blood	Hematopoietic System
25315	25315	SRR25793387	SRX21515627	SRS18742879	SRP457465	PRJNA1010662	The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.	PRJNA1010662	Other	Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.		RNA seq Erythrocytes Wild type embryo	WT embryo	isolate:Wildtype\|age:Embryo\|collection date:N/A\|geo loc name:N/A\|sex:mixed\|tissue:Blood\|BioSampleModel:Model organism or animal									Quant seq Erythrocytes Wild type Danio rerio 2 dpf replicate 1	WT1 embryo blood	WT1 embryo blood	Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457465		DC-WTE1_S13.fastq	fastq	816518564.0	19556325.0	DC WTE1 S13.fastq	0:41.75	A:187091550;C:151287428;G:179967901;T:221475884;N:76695801	41		187091550	151287428	179967901	221475884	76695801	SRX21515627	SRS18742879	SRA1701831	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.61681	0.1874	0.95101	0.56879	29	B	usable mapping rate	illumina	novaseq_era	3prime	poly_a	lexogen	bulk	unknown	unknown	United Kingdom	2023-08-30	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
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
39665	39665	SRR2027911	SRX1029315	SRS937775	SRP058376	PRJNA284108	RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures	GSE68920	Transcriptome Analysis	We used different zebrafish transgenic lines to sort macrophages neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis amplification and library preparation were performed as previously described. Rougeot et al. 2014 Methods Mol Biol 1197:41 66.	pubmed:31832066	6dpf mpeg1:mCherryPosMmarinumGFPPos rep3	GSM1686459	source name:zebra fish larvae\|tissue:20 mpeg1 positive macrophages\|cell population:GFP positive\|developmental stage:6dpf\|caudal vain infection:M marinum M strain 125cfu	6dpf mpeg1:mCherryPosMmarinumGFPPos rep3	Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample	zebra fish larvae	Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.	Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.	Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich	tissue:20 mpeg1 positive macrophages\|cell population:GFP positive\|developmental stage:6dpf\|caudal vain infection:M marinum M strain 125cfu	GSM1686459	GSM1686459: 6dpf mpeg1:mCherryPosMmarinumGFPPos rep3; Danio rerio; RNA Seq	GSM1686459		1	Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.	GEO Accession:GSM1686459	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP058376		ZFG-14-09_06_ATTCCT_L003_R1_001.fastq.gz	fastq	988427889.0	19380939.0	GSM1686459 r1	0:51	A:322268594;C:166925867;G:171531103;T:327506982;N:195343	51		322268594	166925867	171531103	327506982	195343	SRX1029315	SRS937775	SRA268539	GEO	Institute of Biology, Leiden University	1	0.6999	0.24019	0.85358	0.56832	51	B	usable mapping rate	illumina	hiseq_era	full_length	poly_a	smarter	bulk	unknown	unknown	Netherlands	2015-05-15	Larval	Larval	Blood	Hematopoietic System
39666	39666	SRR2027910	SRX1029314	SRS937773	SRP058376	PRJNA284108	RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures	GSE68920	Transcriptome Analysis	We used different zebrafish transgenic lines to sort macrophages neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis amplification and library preparation were performed as previously described. Rougeot et al. 2014 Methods Mol Biol 1197:41 66.	pubmed:31832066	6dpf mpeg1:mCherryPosMmarinumGFPPos rep2	GSM1686458	source name:zebra fish larvae\|tissue:20 mpeg1 positive macrophages\|cell population:GFP positive\|developmental stage:6dpf\|caudal vain infection:M marinum M strain 125cfu	6dpf mpeg1:mCherryPosMmarinumGFPPos rep2	Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample	zebra fish larvae	Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.	Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.	Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich	tissue:20 mpeg1 positive macrophages\|cell population:GFP positive\|developmental stage:6dpf\|caudal vain infection:M marinum M strain 125cfu	GSM1686458	GSM1686458: 6dpf mpeg1:mCherryPosMmarinumGFPPos rep2; Danio rerio; RNA Seq	GSM1686458		1	Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.	GEO Accession:GSM1686458	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP058376		ZFG-14-09_05_ACTGAT_L003_R1_001.fastq.gz	fastq	846771207.0	16603357.0	GSM1686458 r1	0:51	A:268435928;C:150903620;G:153931870;T:273331733;N:168056	51		268435928	150903620	153931870	273331733	168056	SRX1029314	SRS937773	SRA268539	GEO	Institute of Biology, Leiden University	1	0.72025	0.17943	0.87937	0.5683	51	B	usable mapping rate	illumina	hiseq_era	full_length	poly_a	smarter	bulk	unknown	unknown	Netherlands	2015-05-15	Larval	Larval	Blood	Hematopoietic System
39667	39667	SRR2027909	SRX1029313	SRS937774	SRP058376	PRJNA284108	RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures	GSE68920	Transcriptome Analysis	We used different zebrafish transgenic lines to sort macrophages neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis amplification and library preparation were performed as previously described. Rougeot et al. 2014 Methods Mol Biol 1197:41 66.	pubmed:31832066	6dpf mpeg1:mCherryPosMmarinumGFPPos rep1	GSM1686457	source name:zebra fish larvae\|tissue:20 mpeg1 positive macrophages\|cell population:GFP positive\|developmental stage:6dpf\|caudal vain infection:M marinum M strain 125cfu	6dpf mpeg1:mCherryPosMmarinumGFPPos rep1	Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample	zebra fish larvae	Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.	Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.	Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich	tissue:20 mpeg1 positive macrophages\|cell population:GFP positive\|developmental stage:6dpf\|caudal vain infection:M marinum M strain 125cfu	GSM1686457	GSM1686457: 6dpf mpeg1:mCherryPosMmarinumGFPPos rep1; Danio rerio; RNA Seq	GSM1686457		1	Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.	GEO Accession:GSM1686457	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP058376		ZFG-14-09_04_GAGTGG_L003_R1_001.fastq.gz	fastq	807459642.0	15832542.0	GSM1686457 r1	0:51	A:260516660;C:140425216;G:145411663;T:260942267;N:163836	51		260516660	140425216	145411663	260942267	163836	SRX1029313	SRS937774	SRA268539	GEO	Institute of Biology, Leiden University	1	0.7097	0.17187	0.93304	0.64092	51	B	usable mapping rate	illumina	hiseq_era	full_length	poly_a	smarter	bulk	unknown	unknown	Netherlands	2015-05-15	Larval	Larval	Blood	Hematopoietic System
39668	39668	SRR2027908	SRX1029312	SRS937776	SRP058376	PRJNA284108	RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures	GSE68920	Transcriptome Analysis	We used different zebrafish transgenic lines to sort macrophages neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis amplification and library preparation were performed as previously described. Rougeot et al. 2014 Methods Mol Biol 1197:41 66.	pubmed:31832066	6dpf mpeg1:mCherryPos MmarinumGFPNeg rep3	GSM1686456	source name:zebra fish larvae\|tissue:20 mpeg1 positive macrophages\|cell population:GFP negative\|developmental stage:6dpf\|caudal vain infection:M marinum M strain 125cfu	6dpf mpeg1:mCherryPos MmarinumGFPNeg rep3	Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample	zebra fish larvae	Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.	Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.	Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich	tissue:20 mpeg1 positive macrophages\|cell population:GFP negative\|developmental stage:6dpf\|caudal vain infection:M marinum M strain 125cfu	GSM1686456	GSM1686456: 6dpf mpeg1:mCherryPos MmarinumGFPNeg rep3; Danio rerio; RNA Seq	GSM1686456		1	Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.	GEO Accession:GSM1686456	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP058376		ZFG-14-09_03_CGTACG_L003_R1_001.fastq.gz	fastq	1523483526.0	29872226.0	GSM1686456 r1	0:51	A:499019794;C:267493952;G:277264815;T:479405699;N:299266	51		499019794	267493952	277264815	479405699	299266	SRX1029312	SRS937776	SRA268539	GEO	Institute of Biology, Leiden University	1	0.67328	0.15117	0.91179	0.54858	51	B	usable mapping rate	illumina	hiseq_era	full_length	poly_a	smarter	bulk	unknown	unknown	Netherlands	2015-05-15	Larval	Larval	Blood	Hematopoietic System
39669	39669	SRR2027907	SRX1029311	SRS937777	SRP058376	PRJNA284108	RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures	GSE68920	Transcriptome Analysis	We used different zebrafish transgenic lines to sort macrophages neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis amplification and library preparation were performed as previously described. Rougeot et al. 2014 Methods Mol Biol 1197:41 66.	pubmed:31832066	6dpf mpeg1:mCherryPos MmarinumGFPNeg rep2	GSM1686455	source name:zebra fish larvae\|tissue:20 mpeg1 positive macrophages\|cell population:GFP negative\|developmental stage:6dpf\|caudal vain infection:M marinum M strain 125cfu	6dpf mpeg1:mCherryPos MmarinumGFPNeg rep2	Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample	zebra fish larvae	Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.	Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.	Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich	tissue:20 mpeg1 positive macrophages\|cell population:GFP negative\|developmental stage:6dpf\|caudal vain infection:M marinum M strain 125cfu	GSM1686455	GSM1686455: 6dpf mpeg1:mCherryPos MmarinumGFPNeg rep2; Danio rerio; RNA Seq	GSM1686455		1	Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.	GEO Accession:GSM1686455	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP058376		ZFG-14-09_02_GTTTCG_L003_R1_001.fastq.gz	fastq	938675094.0	18405394.0	GSM1686455 r1	0:51	A:284384359;C:173449465;G:178039777;T:302612825;N:188668	51		284384359	173449465	178039777	302612825	188668	SRX1029311	SRS937777	SRA268539	GEO	Institute of Biology, Leiden University	1	0.72884	0.14723	0.90767	0.57414	51	B	usable mapping rate	illumina	hiseq_era	full_length	poly_a	smarter	bulk	unknown	unknown	Netherlands	2015-05-15	Larval	Larval	Blood	Hematopoietic System
39670	39670	SRR2027906	SRX1029310	SRS937778	SRP058376	PRJNA284108	RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures	GSE68920	Transcriptome Analysis	We used different zebrafish transgenic lines to sort macrophages neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis amplification and library preparation were performed as previously described. Rougeot et al. 2014 Methods Mol Biol 1197:41 66.	pubmed:31832066	6dpf mpeg1:mCherryPos MmarinumGFPNeg rep1	GSM1686454	source name:zebra fish larvae\|tissue:20 mpeg1 positive macrophages\|cell population:GFP negative\|developmental stage:6dpf\|caudal vain infection:M marinum M strain 125cfu	6dpf mpeg1:mCherryPos MmarinumGFPNeg rep1	Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample	zebra fish larvae	Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.	Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.	Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich	tissue:20 mpeg1 positive macrophages\|cell population:GFP negative\|developmental stage:6dpf\|caudal vain infection:M marinum M strain 125cfu	GSM1686454	GSM1686454: 6dpf mpeg1:mCherryPos MmarinumGFPNeg rep1; Danio rerio; RNA Seq	GSM1686454		1	Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.	GEO Accession:GSM1686454	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP058376		ZFG-14-09_01_GTGGCC_L003_R1_001.fastq.gz	fastq	1248324348.0	24476948.0	GSM1686454 r1	0:51	A:391067882;C:223380294;G:229132022;T:404526410;N:217740	51		391067882	223380294	229132022	404526410	217740	SRX1029310	SRS937778	SRA268539	GEO	Institute of Biology, Leiden University	1	0.70232	0.14257	0.92894	0.59305	51	B	usable mapping rate	illumina	hiseq_era	full_length	poly_a	smarter	bulk	unknown	unknown	Netherlands	2015-05-15	Larval	Larval	Blood	Hematopoietic System
41032	41032	SRR3581739	SRX1797279	SRS1465200	SRP075626	PRJNA322629	Mycobacterial infection of adult zebrafish	PRJNA322629	Other	RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.		Larval non fluorescent cells post macrophage sorting3	C NF3	breed:*AB\|age:4dpf\|dev stage:Larval\|sex:not determined\|tissue:Whole animal following macrophage depletion via FACS\|BioSampleModel:Model organism or animal									C NF3	C NF3	C NF3	1			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP075626		C_NF3.fastq.gz	fastq	1745512893.0	34225743.0	C NF3.fastq.gz	0:51	A:470456301;C:396221813;G:401458508;T:477287506;N:88765	51		470456301	396221813	401458508	477287506	88765	SRX1797279	SRS1465200	SRA429046	Duke University\|Molecular Genetics & Microbiology	Duke University	1	0.92839	0.06821	0.73099	0.44395	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2016-05-25	Larval	Larval	Blood	Hematopoietic System
41033	41033	SRR3581729	SRX1797278	SRS1465199	SRP075626	PRJNA322629	Mycobacterial infection of adult zebrafish	PRJNA322629	Other	RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.		Larval non fluorescent cells post macrophage sorting2	C NF2	breed:*AB\|age:4dpf\|dev stage:Larval\|sex:not determined\|tissue:Whole animal following macrophage depletion via FACS\|BioSampleModel:Model organism or animal									C NF2	C NF2	C NF2	1			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP075626		C_NF2.fastq.gz	fastq	2116510506.0	41500206.0	C NF2.fastq.gz	0:51	A:580244434;C:475940957;G:474848964;T:585459729;N:16422	51		580244434	475940957	474848964	585459729	16422	SRX1797278	SRS1465199	SRA429045	Duke University\|Molecular Genetics & Microbiology	Duke University	1	0.90388	0.06926	0.78963	0.49501	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2017-06-24	Larval	Larval	Blood	Hematopoietic System
41034	41034	SRR3581718	SRX1797274	SRS1465196	SRP075626	PRJNA322629	Mycobacterial infection of adult zebrafish	PRJNA322629	Other	RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.		Larval non fluorescent cells post macrophage sorting1	C NF1	breed:*AB\|age:4dpf\|dev stage:Larval\|sex:not determined\|tissue:Whole animal following macrophage depletion via FACS\|BioSampleModel:Model organism or animal									C NF1	C NF1	C NF1	1			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP075626		C_NF1.fastq.gz	fastq	1492422690.0	29263190.0	C NF1.fastq.gz	0:51	A:421145406;C:327412398;G:328273236;T:415327504;N:264146	51		421145406	327412398	328273236	415327504	264146	SRX1797274	SRS1465196	SRA429041	Duke University\|Molecular Genetics & Microbiology	Duke University	1	0.82347	0.08561	0.75207	0.45637	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2017-06-24	Larval	Larval	Blood	Hematopoietic System
41038	41038	SRR3581671	SRX1797269	SRS1465191	SRP075626	PRJNA322629	Mycobacterial infection of adult zebrafish	PRJNA322629	Other	RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.		Fluorescence activated cell sorted macrophages1	iRed1	breed:*AB\|dev stage:Adult\|sex:pooled male and female\|tissue:Fluorescence activated cell sorted macrophages\|BioSampleModel:Model organism or animal									iRed1	iRed1	iRed1	1			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP075626		iRed1.fastq.gz	fastq	2227229772.0	43671172.0	iRed1.fastq.gz	0:51	A:643185725;C:477251583;G:480258902;T:626515881;N:17681	51		643185725	477251583	480258902	626515881	17681	SRX1797269	SRS1465191	SRA429036	Duke University\|Molecular Genetics & Microbiology	Duke University	1	0.88005	0.11318	0.76197	0.49474	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2017-06-24	Adult	Adult	Blood	Hematopoietic System
41039	41039	SRR3581670	SRX1797268	SRS1465190	SRP075626	PRJNA322629	Mycobacterial infection of adult zebrafish	PRJNA322629	Other	RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.		D rerio dissected M marinum granuloma5	disGran5	breed:*AB\|dev stage:Adult\|sex:pooled male and female\|tissue:Dissected granuloma\|BioSampleModel:Model organism or animal									disGran5	disGran5	disGran5	1			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP075626		disGran5.fastq.gz	fastq	2097698850.0	41131350.0	disGran5.fastq.gz	0:51	A:606466942;C:449212134;G:448063993;T:593938942;N:16839	51		606466942	449212134	448063993	593938942	16839	SRX1797268	SRS1465190	SRA429035	Duke University\|Molecular Genetics & Microbiology	Duke University	1	0.89212	0.09154	0.76788	0.51096	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2017-06-24	Adult	Adult	Blood	Hematopoietic System
41040	41040	SRR3581669	SRX1797267	SRS1465187	SRP075626	PRJNA322629	Mycobacterial infection of adult zebrafish	PRJNA322629	Other	RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.		D rerio dissected M marinum granuloma4	disGran4	breed:*AB\|dev stage:Adult\|sex:pooled male and female\|tissue:Dissected granuloma\|BioSampleModel:Model organism or animal									disGran4	disGran4	disGran4	1			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP075626		disGran4.fastq.gz	fastq	2969920485.0	58233735.0	disGran4.fastq.gz	0:51	A:861895830;C:635643178;G:635675729;T:836681349;N:24399	51		861895830	635643178	635675729	836681349	24399	SRX1797267	SRS1465187	SRA429034	Duke University\|Molecular Genetics & Microbiology	Duke University	1	0.87215	0.09876	0.7498	0.55116	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2017-06-24	Adult	Adult	Blood	Hematopoietic System
41041	41041	SRR3581668	SRX1797266	SRS1465186	SRP075626	PRJNA322629	Mycobacterial infection of adult zebrafish	PRJNA322629	Other	RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.		D rerio dissected M marinum granuloma3	disGran3	breed:*AB\|dev stage:Adult\|sex:pooled male and female\|tissue:Dissected granuloma\|BioSampleModel:Model organism or animal									disGran3	disGran3	disGran3	1			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP075626		disGran3.fastq.gz	fastq	2398905207.0	47037357.0	disGran3.fastq.gz	0:51	A:693817641;C:513302774;G:516121702;T:675643798;N:19292	51		693817641	513302774	516121702	675643798	19292	SRX1797266	SRS1465186	SRA429033	Duke University\|Molecular Genetics & Microbiology	Duke University	1	0.88631	0.10719	0.75465	0.51255	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2017-06-24	Adult	Adult	Blood	Hematopoietic System
41042	41042	SRR3581667	SRX1797265	SRS1465185	SRP075626	PRJNA322629	Mycobacterial infection of adult zebrafish	PRJNA322629	Other	RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.		D rerio dissected M marinum granuloma2	disGran2	breed:*AB\|dev stage:Adult\|sex:pooled male and female\|tissue:Dissected granuloma\|BioSampleModel:Model organism or animal									disGran2	disGran2	disGran2	1			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP075626		disGran2.fastq.gz	fastq	2108649213.0	41346063.0	disGran2.fastq.gz	0:51	A:606624392;C:457029369;G:459017347;T:585961261;N:16844	51		606624392	457029369	459017347	585961261	16844	SRX1797265	SRS1465185	SRA429032	Duke University\|Molecular Genetics & Microbiology	Duke University	1	0.88259	0.10405	0.74282	0.536	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2017-06-24	Adult	Adult	Blood	Hematopoietic System
41043	41043	SRR3581315	SRX1797076	SRS1465045	SRP075626	PRJNA322629	Mycobacterial infection of adult zebrafish	PRJNA322629	Other	RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.		D rerio dissected M marinum granuloma1	disGran1	breed:*AB\|dev stage:Adult\|sex:pooled male and female\|tissue:Dissected granuloma\|BioSampleModel:Model organism or animal									disGran1	disGran1	disGran1	1			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP075626		disGran1.fastq.gz	fastq	2529627234.0	49600534.0	disGran1.fastq.gz	0:51	A:738849065;C:530442613;G:521673896;T:738641232;N:20428	51		738849065	530442613	521673896	738641232	20428	SRX1797076	SRS1465045	SRA428910	Duke University\|Molecular Genetics & Microbiology	Duke University	1	0.81713	0.09754	0.75213	0.51283	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2017-07-24	Adult	Adult	Blood	Hematopoietic System
51262	51262	SRR8632323	SRX5431024	SRS4411019	SRP186864	PRJNA524286	The miR 199 CDK2 axis modulates neutrophil migration and systemic inflammation	GSE127174	Transcriptome Analysis	We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils and RNAseq for identification of mRNA targets of miRNA 199 in neutrophils Overall design: for miRNA profiles we compared the miRNA present in zebrafish neutrophils and keratinocytes to the whole embryo. for miR 199 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR199 or vector control	pubmed:31451657	lyzC+	GSM3629718	source name:neutrophils\|strain background:AB\|gentoype/variation:wild type\|tissue:neutrophils	lyzC+	Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000 for Samples 6 11. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter: for Samples 1 5: “ alignEndsType EndToEnd outFilterMismatchNmax 1 outFilterMultimapScoreRange 0 outFilterMultimapNmax 10 outSAMunmapped Within outFilterScoreMinOverLread 0 outFilterMatchNminOverLread 0 outFilterMatchNmin 16 alignSJDBoverhangMin 1000” for Samples 6 11: “ outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5: “ s 1 –Q 10” for Samples 6 11 " p Q 10". The data was filtered: for Samples 1 5 using read count > 10 in more than 1 of the samples; for Samples 6 11 using read count per million CPM > 0.5 in more than 3 of the samples normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts	neutrophils	transgenic zebrafish lines were used to produce embryos. For miRNA profiling transgenic lines expressing GFP in either neutrophils or apical keratincyes were used. For miR 199 target discovery transgenic lines expressing miR 199 or a vector control together with a GFP reporter were used.	tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..	zebrafish embryos were grown to 3 dpf in embryonic media	strain background:AB\|gentoype/variation:wild type\|tissue:neutrophils	GSM3629718	GSM3629718: lyzC+; Danio rerio; RNA Seq	GSM3629718		1	tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..	GEO Accession:GSM3629718	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP186864		lyzc.fastq.gz	fastq	98774200.0	1975484.0	GSM3629718 r1	0:50	A:18442541;C:23267011;G:29755652;T:27302395;N:6601	50		18442541	23267011	29755652	27302395	6601	SRX5431024	SRS4411019	SRA852308	GEO	Department of Biological Sciences, Purdue University	1	0.24185	0.03969	0.94708	0.65078	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	trueseq	sc	single_cell_plate	smartseq	United States	2019-02-26	Larval	Larval	Blood	Hematopoietic System
54715	54715	SRR10136115	SRX6864204	SRS5401831	SRP222275	PRJNA566103	Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis	GSE137629	Other	We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group from uninjected fish 70fish/group and from cells in culture in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells	pubmed:31740783	24: PBS injected fish3	GSM4083497	source name:PBS injected fish\|tissue:Hematopoietic tissue without xxx cells\|FISH strain:TGFli1a:EGFP\|age:8 dpf	24: PBS injected fish3	All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name ID reads and normalized comparision between each groups	PBS injected fish		Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at 80 ˚C. The whole process was finished within 30 min. 1000000 Cells in culture were lysized with TRIzol and stored at 80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.	PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation 120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.	tissue:Hematopoietic tissue without xxx cells\|FISH strain:TGFli1a:EGFP\|age:8 dpf	GSM4083497	GSM4083497: 24: PBS injected fish3; Danio rerio; RNA Seq	GSM4083497		1	Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at 80 ˚C. The whole process was finished within 30 min. 1000000 Cells in culture were lysized with TRIzol and stored at 80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.	GEO Accession:GSM4083497	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP222275		ZFG-16-03_24_18845_TGACCA_L001_R1_001.fastq.gz	fastq	175231359.0	3435909.0	GSM4083497 r1	0:51	A:43536404;C:41827219;G:40775397;T:49039258;N:53081	51		43536404	41827219	40775397	49039258	53081	SRX6864204	SRS5401831	SRA963954	GEO	Institute of Biology, Leiden University	1	0.92557	0.08034	0.71354	0.48221	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2019-09-18	Larval	Larval	Blood	Hematopoietic System
54716	54716	SRR10136116	SRX6864204	SRS5401831	SRP222275	PRJNA566103	Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis	GSE137629	Other	We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group from uninjected fish 70fish/group and from cells in culture in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells	pubmed:31740783	24: PBS injected fish3	GSM4083497	source name:PBS injected fish\|tissue:Hematopoietic tissue without xxx cells\|FISH strain:TGFli1a:EGFP\|age:8 dpf	24: PBS injected fish3	All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name ID reads and normalized comparision between each groups	PBS injected fish		Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at 80 ˚C. The whole process was finished within 30 min. 1000000 Cells in culture were lysized with TRIzol and stored at 80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.	PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation 120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.	tissue:Hematopoietic tissue without xxx cells\|FISH strain:TGFli1a:EGFP\|age:8 dpf	GSM4083497	GSM4083497: 24: PBS injected fish3; Danio rerio; RNA Seq	GSM4083497		1	Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at 80 ˚C. The whole process was finished within 30 min. 1000000 Cells in culture were lysized with TRIzol and stored at 80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.	GEO Accession:GSM4083497	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP222275		ZFG-16-03_24_18845_TGACCA_L002_R1_001.fastq.gz	fastq	183497490.0	3597990.0	GSM4083497 r2	0:51	A:45576151;C:43814900;G:42692291;T:51382292;N:31856	51		45576151	43814900	42692291	51382292	31856	SRX6864204	SRS5401831	SRA963954	GEO	Institute of Biology, Leiden University	1	0.92775	0.08176	0.71305	0.47131	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2019-09-18	Larval	Larval	Blood	Hematopoietic System
54717	54717	SRR10136113	SRX6864203	SRS5401830	SRP222275	PRJNA566103	Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis	GSE137629	Other	We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group from uninjected fish 70fish/group and from cells in culture in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells	pubmed:31740783	23: PBS injected fish2	GSM4083496	source name:PBS injected fish\|tissue:Hematopoietic tissue without xxx cells\|FISH strain:TGFli1a:EGFP\|age:8 dpf	23: PBS injected fish2	All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name ID reads and normalized comparision between each groups	PBS injected fish		Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at 80 ˚C. The whole process was finished within 30 min. 1000000 Cells in culture were lysized with TRIzol and stored at 80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.	PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation 120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.	tissue:Hematopoietic tissue without xxx cells\|FISH strain:TGFli1a:EGFP\|age:8 dpf	GSM4083496	GSM4083496: 23: PBS injected fish2; Danio rerio; RNA Seq	GSM4083496		1	Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at 80 ˚C. The whole process was finished within 30 min. 1000000 Cells in culture were lysized with TRIzol and stored at 80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.	GEO Accession:GSM4083496	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP222275		ZFG-16-03_23_18844_CGATGT_L001_R1_001.fastq.gz	fastq	178603683.0	3502033.0	GSM4083496 r1	0:51	A:43615081;C:43303795;G:41835813;T:49795688;N:53306	51		43615081	43303795	41835813	49795688	53306	SRX6864203	SRS5401830	SRA963954	GEO	Institute of Biology, Leiden University	1	0.9227	0.06923	0.72547	0.45761	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2019-09-18	Larval	Larval	Blood	Hematopoietic System
54718	54718	SRR10136114	SRX6864203	SRS5401830	SRP222275	PRJNA566103	Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis	GSE137629	Other	We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group from uninjected fish 70fish/group and from cells in culture in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells	pubmed:31740783	23: PBS injected fish2	GSM4083496	source name:PBS injected fish\|tissue:Hematopoietic tissue without xxx cells\|FISH strain:TGFli1a:EGFP\|age:8 dpf	23: PBS injected fish2	All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name ID reads and normalized comparision between each groups	PBS injected fish		Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at 80 ˚C. The whole process was finished within 30 min. 1000000 Cells in culture were lysized with TRIzol and stored at 80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.	PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation 120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.	tissue:Hematopoietic tissue without xxx cells\|FISH strain:TGFli1a:EGFP\|age:8 dpf	GSM4083496	GSM4083496: 23: PBS injected fish2; Danio rerio; RNA Seq	GSM4083496		1	Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at 80 ˚C. The whole process was finished within 30 min. 1000000 Cells in culture were lysized with TRIzol and stored at 80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.	GEO Accession:GSM4083496	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP222275		ZFG-16-03_23_18844_CGATGT_L002_R1_001.fastq.gz	fastq	186816264.0	3663064.0	GSM4083496 r2	0:51	A:45642596;C:45311565;G:43750888;T:52078681;N:32534	51		45642596	45311565	43750888	52078681	32534	SRX6864203	SRS5401830	SRA963954	GEO	Institute of Biology, Leiden University	1	0.92517	0.07013	0.72561	0.4586	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2019-09-18	Larval	Larval	Blood	Hematopoietic System
54719	54719	SRR10136111	SRX6864202	SRS5401829	SRP222275	PRJNA566103	Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis	GSE137629	Other	We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group from uninjected fish 70fish/group and from cells in culture in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells	pubmed:31740783	22: PBS injected fish1	GSM4083495	source name:PBS injected fish\|tissue:Hematopoietic tissue without xxx cells\|FISH strain:TGFli1a:EGFP\|age:8 dpf	22: PBS injected fish1	All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name ID reads and normalized comparision between each groups	PBS injected fish		Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at 80 ˚C. The whole process was finished within 30 min. 1000000 Cells in culture were lysized with TRIzol and stored at 80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.	PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation 120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.	tissue:Hematopoietic tissue without xxx cells\|FISH strain:TGFli1a:EGFP\|age:8 dpf	GSM4083495	GSM4083495: 22: PBS injected fish1; Danio rerio; RNA Seq	GSM4083495		1	Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at 80 ˚C. The whole process was finished within 30 min. 1000000 Cells in culture were lysized with TRIzol and stored at 80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.	GEO Accession:GSM4083495	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP222275		ZFG-16-03_22_18843_ATTCCT_L001_R1_001.fastq.gz	fastq	338607105.0	6639355.0	GSM4083495 r1	0:51	A:83848769;C:81493095;G:77979951;T:95181006;N:104284	51		83848769	81493095	77979951	95181006	104284	SRX6864202	SRS5401829	SRA963954	GEO	Institute of Biology, Leiden University	1	0.93231	0.07583	0.70784	0.47906	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2019-09-18	Larval	Larval	Blood	Hematopoietic System
54720	54720	SRR10136112	SRX6864202	SRS5401829	SRP222275	PRJNA566103	Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis	GSE137629	Other	We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group from uninjected fish 70fish/group and from cells in culture in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells	pubmed:31740783	22: PBS injected fish1	GSM4083495	source name:PBS injected fish\|tissue:Hematopoietic tissue without xxx cells\|FISH strain:TGFli1a:EGFP\|age:8 dpf	22: PBS injected fish1	All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name ID reads and normalized comparision between each groups	PBS injected fish		Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at 80 ˚C. The whole process was finished within 30 min. 1000000 Cells in culture were lysized with TRIzol and stored at 80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.	PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation 120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.	tissue:Hematopoietic tissue without xxx cells\|FISH strain:TGFli1a:EGFP\|age:8 dpf	GSM4083495	GSM4083495: 22: PBS injected fish1; Danio rerio; RNA Seq	GSM4083495		1	Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at 80 ˚C. The whole process was finished within 30 min. 1000000 Cells in culture were lysized with TRIzol and stored at 80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.	GEO Accession:GSM4083495	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP222275		ZFG-16-03_22_18843_ATTCCT_L002_R1_001.fastq.gz	fastq	351800346.0	6898046.0	GSM4083495 r2	0:51	A:87109106;C:84668841;G:81026500;T:98935234;N:60665	51		87109106	84668841	81026500	98935234	60665	SRX6864202	SRS5401829	SRA963954	GEO	Institute of Biology, Leiden University	1	0.93354	0.07513	0.7049	0.47898	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2019-09-18	Larval	Larval	Blood	Hematopoietic System
54721	54721	SRR10136109	SRX6864201	SRS5401828	SRP222275	PRJNA566103	Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis	GSE137629	Other	We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group from uninjected fish 70fish/group and from cells in culture in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells	pubmed:31740783	27: Metastases3	GSM4083494	source name:PC 3M Pro4 injected fish\|tissue:Metastases at zebrafish caudal hematopoietic tissue\|FISH strain:TGFli1a:EGFP\|age:8 dpf	27: Metastases3	All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name ID reads and normalized comparision between each groups	PC 3M Pro4 injected fish		Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at 80 ˚C. The whole process was finished within 30 min. 1000000 Cells in culture were lysized with TRIzol and stored at 80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.	PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation 120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.	tissue:Metastases at zebrafish caudal hematopoietic tissue\|FISH strain:TGFli1a:EGFP\|age:8 dpf	GSM4083494	GSM4083494: 27: Metastases3; Danio rerio; Homo sapiens; RNA Seq	GSM4083494		1	Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at 80 ˚C. The whole process was finished within 30 min. 1000000 Cells in culture were lysized with TRIzol and stored at 80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.	GEO Accession:GSM4083494	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP222275		ZFG-16-03_27_19265_CAGATC_L001_R1_001.fastq.gz	fastq	331816863.0	6506213.0	GSM4083494 r1	0:51	A:82933253;C:78905859;G:76570035;T:93218124;N:189592	51		82933253	78905859	76570035	93218124	189592	SRX6864201	SRS5401828	SRA963954	GEO	Institute of Biology, Leiden University	1	0.81726	0.07727	0.71928	0.47447	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2019-09-18	Larval	Larval	Blood	Hematopoietic System
54722	54722	SRR10136110	SRX6864201	SRS5401828	SRP222275	PRJNA566103	Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis	GSE137629	Other	We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group from uninjected fish 70fish/group and from cells in culture in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells	pubmed:31740783	27: Metastases3	GSM4083494	source name:PC 3M Pro4 injected fish\|tissue:Metastases at zebrafish caudal hematopoietic tissue\|FISH strain:TGFli1a:EGFP\|age:8 dpf	27: Metastases3	All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name ID reads and normalized comparision between each groups	PC 3M Pro4 injected fish		Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at 80 ˚C. The whole process was finished within 30 min. 1000000 Cells in culture were lysized with TRIzol and stored at 80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.	PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation 120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.	tissue:Metastases at zebrafish caudal hematopoietic tissue\|FISH strain:TGFli1a:EGFP\|age:8 dpf	GSM4083494	GSM4083494: 27: Metastases3; Danio rerio; Homo sapiens; RNA Seq	GSM4083494		1	Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at 80 ˚C. The whole process was finished within 30 min. 1000000 Cells in culture were lysized with TRIzol and stored at 80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.	GEO Accession:GSM4083494	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP222275		ZFG-16-03_27_19265_CAGATC_L002_R1_001.fastq.gz	fastq	345788568.0	6780168.0	GSM4083494 r2	0:51	A:86481669;C:82220901;G:79836085;T:97146784;N:103129	51		86481669	82220901	79836085	97146784	103129	SRX6864201	SRS5401828	SRA963954	GEO	Institute of Biology, Leiden University	1	0.81844	0.07678	0.7189	0.4755	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2019-09-18	Larval	Larval	Blood	Hematopoietic System
54723	54723	SRR10136107	SRX6864200	SRS5401827	SRP222275	PRJNA566103	Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis	GSE137629	Other	We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group from uninjected fish 70fish/group and from cells in culture in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells	pubmed:31740783	26: Metastases2	GSM4083493	source name:PC 3M Pro4 injected fish\|tissue:Metastases at zebrafish caudal hematopoietic tissue\|FISH strain:TGFli1a:EGFP\|age:8 dpf	26: Metastases2	All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name ID reads and normalized comparision between each groups	PC 3M Pro4 injected fish		Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at 80 ˚C. The whole process was finished within 30 min. 1000000 Cells in culture were lysized with TRIzol and stored at 80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.	PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation 120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.	tissue:Metastases at zebrafish caudal hematopoietic tissue\|FISH strain:TGFli1a:EGFP\|age:8 dpf	GSM4083493	GSM4083493: 26: Metastases2; Danio rerio; Homo sapiens; RNA Seq	GSM4083493		1	Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at 80 ˚C. The whole process was finished within 30 min. 1000000 Cells in culture were lysized with TRIzol and stored at 80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.	GEO Accession:GSM4083493	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP222275		ZFG-16-03_26_19264_GCCAAT_L001_R1_001.fastq.gz	fastq	381088575.0	7472325.0	GSM4083493 r1	0:51	A:93834091;C:91635540;G:89019328;T:106380009;N:219607	51		93834091	91635540	89019328	106380009	219607	SRX6864200	SRS5401827	SRA963954	GEO	Institute of Biology, Leiden University	1	0.79302	0.0612	0.72803	0.47524	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2019-09-18	Larval	Larval	Blood	Hematopoietic System
54724	54724	SRR10136108	SRX6864200	SRS5401827	SRP222275	PRJNA566103	Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis	GSE137629	Other	We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group from uninjected fish 70fish/group and from cells in culture in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells	pubmed:31740783	26: Metastases2	GSM4083493	source name:PC 3M Pro4 injected fish\|tissue:Metastases at zebrafish caudal hematopoietic tissue\|FISH strain:TGFli1a:EGFP\|age:8 dpf	26: Metastases2	All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name ID reads and normalized comparision between each groups	PC 3M Pro4 injected fish		Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at 80 ˚C. The whole process was finished within 30 min. 1000000 Cells in culture were lysized with TRIzol and stored at 80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.	PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation 120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.	tissue:Metastases at zebrafish caudal hematopoietic tissue\|FISH strain:TGFli1a:EGFP\|age:8 dpf	GSM4083493	GSM4083493: 26: Metastases2; Danio rerio; Homo sapiens; RNA Seq	GSM4083493		1	Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at 80 ˚C. The whole process was finished within 30 min. 1000000 Cells in culture were lysized with TRIzol and stored at 80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.	GEO Accession:GSM4083493	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP222275		ZFG-16-03_26_19264_GCCAAT_L002_R1_001.fastq.gz	fastq	396777450.0	7779950.0	GSM4083493 r2	0:51	A:97747141;C:95409433;G:92718325;T:110778709;N:123842	51		97747141	95409433	92718325	110778709	123842	SRX6864200	SRS5401827	SRA963954	GEO	Institute of Biology, Leiden University	1	0.79294	0.06073	0.72636	0.47389	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2019-09-18	Larval	Larval	Blood	Hematopoietic System
54725	54725	SRR10136105	SRX6864199	SRS5401826	SRP222275	PRJNA566103	Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis	GSE137629	Other	We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group from uninjected fish 70fish/group and from cells in culture in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells	pubmed:31740783	25: Metastases1	GSM4083492	source name:PC 3M Pro4 injected fish\|tissue:Metastases at zebrafish caudal hematopoietic tissue\|FISH strain:TGFli1a:EGFP\|age:8 dpf	25: Metastases1	All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name ID reads and normalized comparision between each groups	PC 3M Pro4 injected fish		Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at 80 ˚C. The whole process was finished within 30 min. 1000000 Cells in culture were lysized with TRIzol and stored at 80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.	PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation 120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.	tissue:Metastases at zebrafish caudal hematopoietic tissue\|FISH strain:TGFli1a:EGFP\|age:8 dpf	GSM4083492	GSM4083492: 25: Metastases1; Danio rerio; Homo sapiens; RNA Seq	GSM4083492		1	Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at 80 ˚C. The whole process was finished within 30 min. 1000000 Cells in culture were lysized with TRIzol and stored at 80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.	GEO Accession:GSM4083492	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP222275		ZFG-16-03_25_19263_ACAGTG_L001_R1_001.fastq.gz	fastq	335771148.0	6583748.0	GSM4083492 r1	0:51	A:82544663;C:80955820;G:79009084;T:93066010;N:195571	51		82544663	80955820	79009084	93066010	195571	SRX6864199	SRS5401826	SRA963954	GEO	Institute of Biology, Leiden University	1	0.82172	0.05893	0.72088	0.48241	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2019-09-18	Larval	Larval	Blood	Hematopoietic System
54726	54726	SRR10136106	SRX6864199	SRS5401826	SRP222275	PRJNA566103	Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis	GSE137629	Other	We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group from uninjected fish 70fish/group and from cells in culture in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells	pubmed:31740783	25: Metastases1	GSM4083492	source name:PC 3M Pro4 injected fish\|tissue:Metastases at zebrafish caudal hematopoietic tissue\|FISH strain:TGFli1a:EGFP\|age:8 dpf	25: Metastases1	All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name ID reads and normalized comparision between each groups	PC 3M Pro4 injected fish		Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at 80 ˚C. The whole process was finished within 30 min. 1000000 Cells in culture were lysized with TRIzol and stored at 80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.	PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation 120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.	tissue:Metastases at zebrafish caudal hematopoietic tissue\|FISH strain:TGFli1a:EGFP\|age:8 dpf	GSM4083492	GSM4083492: 25: Metastases1; Danio rerio; Homo sapiens; RNA Seq	GSM4083492		1	Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at 80 ˚C. The whole process was finished within 30 min. 1000000 Cells in culture were lysized with TRIzol and stored at 80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.	GEO Accession:GSM4083492	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP222275		ZFG-16-03_25_19263_ACAGTG_L002_R1_001.fastq.gz	fastq	348764061.0	6838511.0	GSM4083492 r2	0:51	A:85790391;C:84069256;G:82076851;T:96714974;N:112589	51		85790391	84069256	82076851	96714974	112589	SRX6864199	SRS5401826	SRA963954	GEO	Institute of Biology, Leiden University	1	0.82119	0.06015	0.72299	0.47492	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2019-09-18	Larval	Larval	Blood	Hematopoietic System
55536	55536	SRR10532692	SRX7216663	SRS5719129	SRP233258	PRJNA591815	Ago2 dependent processing allows miR 451 to evade the global microRNA turnover elicited during erythropoiesis	PRJNA591815	Other	MicroRNAs are sequentially processed by two RNAse III enzymes Drosha and Dicer. miR 451 is the only known miRNA whose processing bypasses Dicer and instead relies on the slicer activity of Argonaute 2 Ago2. MiR 451 is highly conserved in vertebrates and regulates erythrocyte maturation where it becomes the most abundant miRNA. However the basis for the non canonical biogenesis of miR 451 is unclear. In this study we tested the hypothesis that miR 144 represses Dicer in a negative feedback loop during erythropoiesis and enhances miR 451 biogenesis. Loss of miR 144 mediated Dicer repression in zebrafish embryos and human cells leads to increased canonical miRNA production and impaired miR 451 maturation.			miR 451 mutant	isolate:Lab reared\|age:2 days\|sex:not applicable\|tissue:peripheral blood\|genotype:miR 451 / \|phenotype:wild type\|treatment:n1\|BioSampleModel:Model organism or animal									Transcriptomic profiling of peripheral blood from 2 dpf zebrafish embryos	mRNA Mut miR 451	mRNA Mut miR 451	mRNA libraries were cloned from polyA+ RNA isolated from peripheral blood of 2 dpf WT and mutant zebrafish embryos according to Illumina TruSeq protocol. Libraries were cloned and sequenced at Boston University Microarray and Sequencing core.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	NextSeq 500	SRP233258		mRNA-miR-451.fastq.gz	fastq	7904410367.0	104613601.0	mRNA miR 451.fastq.gz	0:75.56 1:0	A:1795110678;C:2004074141;G:2113982350;T:1989843693;N:1399505	75	0	1795110678	2004074141	2113982350	1989843693	1399505	SRX7216663	SRS5719129	SRA1002853	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.97314	0.03847	0.81744	0.4673	75	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	United Kingdom	2019-11-26	Hatching	Embryo	Blood	Hematopoietic System
55537	55537	SRR10532693	SRX7216662	SRS5719128	SRP233258	PRJNA591815	Ago2 dependent processing allows miR 451 to evade the global microRNA turnover elicited during erythropoiesis	PRJNA591815	Other	MicroRNAs are sequentially processed by two RNAse III enzymes Drosha and Dicer. miR 451 is the only known miRNA whose processing bypasses Dicer and instead relies on the slicer activity of Argonaute 2 Ago2. MiR 451 is highly conserved in vertebrates and regulates erythrocyte maturation where it becomes the most abundant miRNA. However the basis for the non canonical biogenesis of miR 451 is unclear. In this study we tested the hypothesis that miR 144 represses Dicer in a negative feedback loop during erythropoiesis and enhances miR 451 biogenesis. Loss of miR 144 mediated Dicer repression in zebrafish embryos and human cells leads to increased canonical miRNA production and impaired miR 451 maturation.			miR 144 mutant	isolate:Lab reared\|age:2 days\|sex:not applicable\|tissue:peripheral blood\|genotype:miR 144 / \|phenotype:wild type\|treatment:n1\|BioSampleModel:Model organism or animal									Transcriptomic profiling of peripheral blood from 2 dpf zebrafish embryos	mRNA Mut miR 144	mRNA Mut miR 144	mRNA libraries were cloned from polyA+ RNA isolated from peripheral blood of 2 dpf WT and mutant zebrafish embryos according to Illumina TruSeq protocol. Libraries were cloned and sequenced at Boston University Microarray and Sequencing core.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	NextSeq 500	SRP233258		mRNA-miR-144.fastq.gz	fastq	21666521349.0	286736059.0	mRNA miR 144.fastq.gz	0:75.56 1:0	A:4937891523;C:5429635867;G:5884853915;T:5410789187;N:3350857	75	0	4937891523	5429635867	5884853915	5410789187	3350857	SRX7216662	SRS5719128	SRA1002853	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.97729	0.02379	0.84102	0.45517	76	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	United Kingdom	2019-11-26	Hatching	Embryo	Blood	Hematopoietic System
55538	55538	SRR10532694	SRX7216661	SRS5719127	SRP233258	PRJNA591815	Ago2 dependent processing allows miR 451 to evade the global microRNA turnover elicited during erythropoiesis	PRJNA591815	Other	MicroRNAs are sequentially processed by two RNAse III enzymes Drosha and Dicer. miR 451 is the only known miRNA whose processing bypasses Dicer and instead relies on the slicer activity of Argonaute 2 Ago2. MiR 451 is highly conserved in vertebrates and regulates erythrocyte maturation where it becomes the most abundant miRNA. However the basis for the non canonical biogenesis of miR 451 is unclear. In this study we tested the hypothesis that miR 144 represses Dicer in a negative feedback loop during erythropoiesis and enhances miR 451 biogenesis. Loss of miR 144 mediated Dicer repression in zebrafish embryos and human cells leads to increased canonical miRNA production and impaired miR 451 maturation.			wild type	isolate:Lab reared\|age:2 days\|sex:not applicable\|tissue:peripheral blood\|genotype:wild type\|phenotype:wild type\|treatment:n1\|BioSampleModel:Model organism or animal									Transcriptomic profiling of peripheral blood from 2 dpf zebrafish embryos	mRNA WT	mRNA WT	mRNA libraries were cloned from polyA+ RNA isolated from peripheral blood of 2 dpf WT and mutant zebrafish embryos according to Illumina TruSeq protocol. Libraries were cloned and sequenced at Boston University Microarray and Sequencing core.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	NextSeq 500	SRP233258		mRNA-WT.fastq.gz	fastq	5359234061.0	70925969.0	mRNA WT.fastq.gz	0:75.56 1:0	A:1229417939;C:1341096472;G:1448568683;T:1339375309;N:775658	75	0	1229417939	1341096472	1448568683	1339375309	775658	SRX7216661	SRS5719127	SRA1002853	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.97314	0.02809	0.83179	0.40499	75	B	usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown	United Kingdom	2019-11-26	Hatching	Embryo	Blood	Hematopoietic System
55539	55539	SRR10532695	SRX7216660	SRS5719128	SRP233258	PRJNA591815	Ago2 dependent processing allows miR 451 to evade the global microRNA turnover elicited during erythropoiesis	PRJNA591815	Other	MicroRNAs are sequentially processed by two RNAse III enzymes Drosha and Dicer. miR 451 is the only known miRNA whose processing bypasses Dicer and instead relies on the slicer activity of Argonaute 2 Ago2. MiR 451 is highly conserved in vertebrates and regulates erythrocyte maturation where it becomes the most abundant miRNA. However the basis for the non canonical biogenesis of miR 451 is unclear. In this study we tested the hypothesis that miR 144 represses Dicer in a negative feedback loop during erythropoiesis and enhances miR 451 biogenesis. Loss of miR 144 mediated Dicer repression in zebrafish embryos and human cells leads to increased canonical miRNA production and impaired miR 451 maturation.			miR 144 mutant	isolate:Lab reared\|age:2 days\|sex:not applicable\|tissue:peripheral blood\|genotype:miR 144 / \|phenotype:wild type\|treatment:n1\|BioSampleModel:Model organism or animal									Small RNA from peripheral blood from 2 dpf zebrafish embryos miR 451 mutant	sRNA Mut miR 144	sRNA Mut miR 144	Small RNA libraries were prepared from total RNA 0.5 g isolated from peripheral blood of wild type WT and miR 144 / embryos at 48 hpf Small RNAs were size selected in 10% denaturing polyacrylamide gel in 1X TBE in range from 18 to 75 bp. RNA extraction from the gel was achieved by incubation in 0.3 M NaCl overnight at 4C with following precipitation with isopropanol. Pre adenylated 3 custom adaptor WT: /5PHOS/NNCACAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3ddC/; miR 144 / :/5PHOS/NNAGAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3ddC/ were ligated to small RNAs by T4 RNA ligase for 2 h at 22 C. post ligated products were size selected by gel from non ligated adaptor. Reverse transcription was performed by SuperScript III Reverse Transcription kit Thermo Fisher using custom RT Cloning Primer /5PHOS/NNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC SPC18 GGATCC SPC18 GTGACTGGAGTTCAGACGTGTGCTC. Then cDNA products were isolated by gel selection and then circularized by CircLigase ssDNA Ligase Epicentre. cDNA libraries were amplified in reactions containing forward and reverse Illumina index primers.			miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 500	SRP233258		sRNA-miR-144.fastq.gz	fastq	284208421.0	7813754.0	sRNA miR 144.fastq.gz	0:36.37	A:63063755;C:66933795;G:92235682;T:61966771;N:8418	36		63063755	66933795	92235682	61966771	8418	SRX7216660	SRS5719128	SRA1002853	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.02041	0.00444	0.98512	0.44771	28	B	usable mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	United Kingdom	2019-11-26	Hatching	Embryo	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");;