metadata: run_metadata: 352 rows where experiment.library_layout = "SINGLE", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation

352 rows where experiment.library_layout = "SINGLE", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation_coarse = "Hematopoietic System"

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.spot_descriptor	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.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
38293	38293	SRR1647684	SRX756919	SRS742121	SRP049663	PRJNA266803	Spring Varaemia of Carp Virus SVCV infection of adult zebrafish	GSE63133	Transcriptome Analysis	During viral infection a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection i.e. 6h and 24h post infection. For 12 zebrafish IRFs we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7 which together with DrIRF3 was highly induced by SVCV infection. For type I IFNs zebrafish has four IFN genes three of which IFN1/2/3 particularly IFN 1 and IFN 3 were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately 50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.	pubmed:25535281	24S	GSM1541908	source name:spleen\|tissue:spleen\|disease state:24h post SVCV infection	24S	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	spleen		Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:spleen\|disease state:24h post SVCV infection	GSM1541908	GSM1541908: 24S; Danio rerio; RNA Seq	GSM1541908		1	Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM1541908	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP049663		24S_ATGTCA_L003_R1.fastq	fastq	1207014756.0	23666956.0	GSM1541908 r1	0:51	A:316359100;C:290453604;G:283305513;T:316815698;N:80841	51	316359100	290453604	283305513	316815698	80841	SRX756919	SRS742121	SRA200717	GEO	Institute of Hydrobiology, Chinese Academy of Sciences	1	0.91158	0.09021	0.70867	0.46907	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	China	2014-11-10	Undetermined	Adult	Spleen	Hematopoietic System
38294	38294	SRR1647683	SRX756918	SRS742119	SRP049663	PRJNA266803	Spring Varaemia of Carp Virus SVCV infection of adult zebrafish	GSE63133	Transcriptome Analysis	During viral infection a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection i.e. 6h and 24h post infection. For 12 zebrafish IRFs we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7 which together with DrIRF3 was highly induced by SVCV infection. For type I IFNs zebrafish has four IFN genes three of which IFN1/2/3 particularly IFN 1 and IFN 3 were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately 50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.	pubmed:25535281	6S	GSM1541907	source name:spleen\|tissue:spleen\|disease state:6h post SVCV infection	6S	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	spleen		Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:spleen\|disease state:6h post SVCV infection	GSM1541907	GSM1541907: 6S; Danio rerio; RNA Seq	GSM1541907		1	Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM1541907	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP049663		6S_AGTTCC_L003_R1.fastq	fastq	1251006540.0	24529540.0	GSM1541907 r1	0:51	A:323805792;C:303846999;G:297418642;T:325862442;N:72665	51	323805792	303846999	297418642	325862442	72665	SRX756918	SRS742119	SRA200717	GEO	Institute of Hydrobiology, Chinese Academy of Sciences	1	0.92105	0.09005	0.71273	0.46937	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	China	2014-11-10	Undetermined	Adult	Spleen	Hematopoietic System
38295	38295	SRR1647682	SRX756917	SRS742118	SRP049663	PRJNA266803	Spring Varaemia of Carp Virus SVCV infection of adult zebrafish	GSE63133	Transcriptome Analysis	During viral infection a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection i.e. 6h and 24h post infection. For 12 zebrafish IRFs we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7 which together with DrIRF3 was highly induced by SVCV infection. For type I IFNs zebrafish has four IFN genes three of which IFN1/2/3 particularly IFN 1 and IFN 3 were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately 50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.	pubmed:25535281	0S	GSM1541906	source name:spleen\|tissue:spleen\|disease state:un infected	0S	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	spleen		Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:spleen\|disease state:un infected	GSM1541906	GSM1541906: 0S; Danio rerio; RNA Seq	GSM1541906		1	Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM1541906	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP049663		0S_AGTCAA_L003_R1.fastq	fastq	1155087372.0	22648772.0	GSM1541906 r1	0:51	A:301183546;C:279328135;G:272663981;T:301834798;N:76912	51	301183546	279328135	272663981	301834798	76912	SRX756917	SRS742118	SRA200717	GEO	Institute of Hydrobiology, Chinese Academy of Sciences	1	0.91841	0.09679	0.70546	0.47624	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	China	2014-11-10	Undetermined	Adult	Spleen	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
39974	39974	SRR2726604	SRX1354695	SRS1121101	SRP064895	PRJNA298967	Danio rerio Raw sequence reads	PRJNA298967	Whole Genome Sequencing	Alternative polyadenylation in the anti bacterial immune response of zebrafish			UC.fq.gz	breed:missing\|cultivar:missing\|ecotype:missing\|isolate:missing\|strain:missing\|age:6 month\|dev stage:adult\|sex:male\|tissue:spleen\|BioSampleModel:Model organism or animal									Alternative polyadenylation in the anti bacterial immune response of zebrafish	UC	298967	SAPAS three prime cDNA library			RNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>55</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP064895		UC.fq.gz	fastq	908330752.0	16220192.0	UC	0:56	A:268296300;C:164753303;G:152582935;T:321764605;N:933609	56	268296300	164753303	152582935	321764605	933609	SRX1354695	SRS1121101	SRA305678	Sun Yat-Sen University\|Department of Biochemistry, College of Life Scienc	Sun Yat-Sen University	1	0.76113	0.14836	0.86764	0.49191	56	B	usable mapping rate	illumina	early_illumina	unknown	random_priming	unknown	bulk	unknown	unknown	China	2015-10-19	Adult	Adult	Spleen	Hematopoietic System
39975	39975	SRR2726605	SRX1343023	SRS1117908	SRP064895	PRJNA298967	Danio rerio Raw sequence reads	PRJNA298967	Whole Genome Sequencing	Alternative polyadenylation in the anti bacterial immune response of zebrafish			BC.fq.gz	breed:missing\|cultivar:missing\|ecotype:missing\|isolate:missing\|strain:missing\|age:6 month\|dev stage:adult\|sex:male\|tissue:spleen\|health state:health\|sample type:tissue sample\|BioSampleModel:Model organism or animal									Alternative polyadenylation in the anti bacterial immune response of zebrafish	298967	298967	SAPAS three prime cDNA library			RNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>55</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP064895		BC.fq.gz	fastq	613456536.0	10954581.0	BC	0:56	A:184952368;C:111595938;G:99647506;T:216155456;N:1105268	56	184952368	111595938	99647506	216155456	1105268	SRX1343023	SRS1117908	SRA305678	Sun Yat-Sen University\|Department of Biochemistry, College of Life Scienc	Sun Yat-Sen University	1	0.74636	0.11848	0.84678	0.47133	56	B	usable mapping rate	illumina	early_illumina	unknown	random_priming	unknown	bulk	unknown	unknown	China	2015-10-24	Adult	Adult	Spleen	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
47583	47583	SRR6661157	SRX3638253	SRS2904504	SRP131956	PRJNA432507	Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne	GSE109978	Transcriptome Analysis	RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.	pubmed:30248094	SplWTPHZ 3	GSM2975201	source name:whole animal\|tissue:spleen\|age:5 mpf 6 mpf\|genotype:Wild type	SplWTPHZ 3	Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.	whole animal	Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	Normal zebrafish husbandary	tissue:spleen\|age:5 mpf 6 mpf\|genotype:Wild type	GSM2975201	GSM2975201: SplWTPHZ 3; Danio rerio; RNA Seq	GSM2975201		1	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	GEO Accession:GSM2975201	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP131956		SplWTPHZ_3.fastq.gz	fastq	863137362.0	16924262.0	GSM2975201 r1	0:51	A:243029420;C:186621398;G:190769119;T:242704294;N:13131	51	243029420	186621398	190769119	242704294	13131	SRX3638253	SRS2904504	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.94871	0.18797	0.7289	0.48689	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Spleen	Hematopoietic System
47584	47584	SRR6661156	SRX3638252	SRS2904503	SRP131956	PRJNA432507	Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne	GSE109978	Transcriptome Analysis	RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.	pubmed:30248094	SplWTPHZ 2	GSM2975200	source name:whole animal\|tissue:spleen\|age:5 mpf 6 mpf\|genotype:Wild type	SplWTPHZ 2	Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.	whole animal	Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	Normal zebrafish husbandary	tissue:spleen\|age:5 mpf 6 mpf\|genotype:Wild type	GSM2975200	GSM2975200: SplWTPHZ 2; Danio rerio; RNA Seq	GSM2975200		1	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	GEO Accession:GSM2975200	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP131956		SplWTPHZ_2.fastq.gz	fastq	748057494.0	14667794.0	GSM2975200 r1	0:51	A:212731080;C:159238564;G:163993235;T:212082953;N:11662	51	212731080	159238564	163993235	212082953	11662	SRX3638252	SRS2904503	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.94641	0.22364	0.7264	0.48998	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Spleen	Hematopoietic System
47585	47585	SRR6661155	SRX3638251	SRS2904502	SRP131956	PRJNA432507	Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne	GSE109978	Transcriptome Analysis	RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.	pubmed:30248094	SplWTPHZ 1	GSM2975199	source name:whole animal\|tissue:spleen\|age:5 mpf 6 mpf\|genotype:Wild type	SplWTPHZ 1	Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.	whole animal	Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	Normal zebrafish husbandary	tissue:spleen\|age:5 mpf 6 mpf\|genotype:Wild type	GSM2975199	GSM2975199: SplWTPHZ 1; Danio rerio; RNA Seq	GSM2975199		1	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	GEO Accession:GSM2975199	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP131956		SplWTPHZ_1.fastq.gz	fastq	771862917.0	15134567.0	GSM2975199 r1	0:51	A:220317243;C:164032479;G:167543123;T:219958265;N:11807	51	220317243	164032479	167543123	219958265	11807	SRX3638251	SRS2904502	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.94835	0.1926	0.71453	0.48677	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Spleen	Hematopoietic System
47586	47586	SRR6661154	SRX3638250	SRS2904501	SRP131956	PRJNA432507	Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne	GSE109978	Transcriptome Analysis	RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.	pubmed:30248094	SplWT 3	GSM2975198	source name:whole animal\|tissue:spleen\|age:5 mpf 6 mpf\|genotype:Wild type	SplWT 3	Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.	whole animal	Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	Normal zebrafish husbandary	tissue:spleen\|age:5 mpf 6 mpf\|genotype:Wild type	GSM2975198	GSM2975198: SplWT 3; Danio rerio; RNA Seq	GSM2975198		1	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	GEO Accession:GSM2975198	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP131956		SplWT_3.fastq.gz	fastq	815973888.0	15999488.0	GSM2975198 r1	0:51	A:236186435;C:169473350;G:175246943;T:235055142;N:12018	51	236186435	169473350	175246943	235055142	12018	SRX3638250	SRS2904501	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.94554	0.25855	0.71873	0.54675	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Spleen	Hematopoietic System
47587	47587	SRR6661153	SRX3638249	SRS2904499	SRP131956	PRJNA432507	Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne	GSE109978	Transcriptome Analysis	RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.	pubmed:30248094	SplWT 2	GSM2975197	source name:whole animal\|tissue:spleen\|age:5 mpf 6 mpf\|genotype:Wild type	SplWT 2	Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.	whole animal	Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	Normal zebrafish husbandary	tissue:spleen\|age:5 mpf 6 mpf\|genotype:Wild type	GSM2975197	GSM2975197: SplWT 2; Danio rerio; RNA Seq	GSM2975197		1	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	GEO Accession:GSM2975197	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP131956		SplWT_2.fastq.gz	fastq	909644262.0	17836162.0	GSM2975197 r1	0:51	A:259661486;C:192636111;G:198048163;T:259284494;N:14008	51	259661486	192636111	198048163	259284494	14008	SRX3638249	SRS2904499	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.94781	0.22979	0.69962	0.49839	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Spleen	Hematopoietic System
47588	47588	SRR6661152	SRX3638248	SRS2904500	SRP131956	PRJNA432507	Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne	GSE109978	Transcriptome Analysis	RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.	pubmed:30248094	SplWT 1	GSM2975196	source name:whole animal\|tissue:spleen\|age:5 mpf 6 mpf\|genotype:Wild type	SplWT 1	Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.	whole animal	Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	Normal zebrafish husbandary	tissue:spleen\|age:5 mpf 6 mpf\|genotype:Wild type	GSM2975196	GSM2975196: SplWT 1; Danio rerio; RNA Seq	GSM2975196		1	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	GEO Accession:GSM2975196	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP131956		SplWT_1.fastq.gz	fastq	888755274.0	17426574.0	GSM2975196 r1	0:51	A:241072815;C:200347978;G:205733626;T:241587449;N:13406	51	241072815	200347978	205733626	241587449	13406	SRX3638248	SRS2904500	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.95759	0.1342	0.72918	0.52233	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Spleen	Hematopoietic System
47589	47589	SRR6661151	SRX3638247	SRS2904498	SRP131956	PRJNA432507	Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne	GSE109978	Transcriptome Analysis	RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.	pubmed:30248094	SplDKOPHZ 3	GSM2975195	source name:whole animal\|tissue:spleen\|age:5 mpf 6 mpf\|genotype:Tu/hrg1 doulble knockout DKO	SplDKOPHZ 3	Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.	whole animal	Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	Normal zebrafish husbandary	tissue:spleen\|age:5 mpf 6 mpf\|genotype:Tu/hrg1 doulble knockout DKO	GSM2975195	GSM2975195: SplDKOPHZ 3; Danio rerio; RNA Seq	GSM2975195		1	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	GEO Accession:GSM2975195	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP131956		SplDKOPHZ_3.fastq.gz	fastq	881441160.0	17283160.0	GSM2975195 r1	0:51	A:243254581;C:194198200;G:199055092;T:244919975;N:13312	51	243254581	194198200	199055092	244919975	13312	SRX3638247	SRS2904498	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.90441	0.14881	0.71447	0.51129	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Spleen	Hematopoietic System
47590	47590	SRR6661150	SRX3638246	SRS2904497	SRP131956	PRJNA432507	Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne	GSE109978	Transcriptome Analysis	RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.	pubmed:30248094	SplDKOPHZ 2	GSM2975194	source name:whole animal\|tissue:spleen\|age:5 mpf 6 mpf\|genotype:Tu/hrg1 doulble knockout DKO	SplDKOPHZ 2	Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.	whole animal	Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	Normal zebrafish husbandary	tissue:spleen\|age:5 mpf 6 mpf\|genotype:Tu/hrg1 doulble knockout DKO	GSM2975194	GSM2975194: SplDKOPHZ 2; Danio rerio; RNA Seq	GSM2975194		1	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	GEO Accession:GSM2975194	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP131956		SplDKOPHZ_2.fastq.gz	fastq	795840414.0	15604714.0	GSM2975194 r1	0:51	A:229921467;C:166126021;G:170186584;T:229594266;N:12076	51	229921467	166126021	170186584	229594266	12076	SRX3638246	SRS2904497	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.88657	0.23556	0.7194	0.51207	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Spleen	Hematopoietic System
47591	47591	SRR6661149	SRX3638245	SRS2904495	SRP131956	PRJNA432507	Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne	GSE109978	Transcriptome Analysis	RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.	pubmed:30248094	SplDKOPHZ 1	GSM2975193	source name:whole animal\|tissue:spleen\|age:5 mpf 6 mpf\|genotype:Tu/hrg1 doulble knockout DKO	SplDKOPHZ 1	Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.	whole animal	Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	Normal zebrafish husbandary	tissue:spleen\|age:5 mpf 6 mpf\|genotype:Tu/hrg1 doulble knockout DKO	GSM2975193	GSM2975193: SplDKOPHZ 1; Danio rerio; RNA Seq	GSM2975193		1	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	GEO Accession:GSM2975193	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP131956		SplDKOPHZ_1.fastq.gz	fastq	788951436.0	15469636.0	GSM2975193 r1	0:51	A:217408862;C:175236911;G:178930271;T:217363444;N:11948	51	217408862	175236911	178930271	217363444	11948	SRX3638245	SRS2904495	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.90945	0.10065	0.72468	0.48596	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Spleen	Hematopoietic System
47592	47592	SRR6661148	SRX3638244	SRS2904496	SRP131956	PRJNA432507	Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne	GSE109978	Transcriptome Analysis	RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.	pubmed:30248094	SplDKO 3	GSM2975192	source name:whole animal\|tissue:spleen\|age:5 mpf 6 mpf\|genotype:Tu/hrg1 doulble knockout DKO	SplDKO 3	Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.	whole animal	Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	Normal zebrafish husbandary	tissue:spleen\|age:5 mpf 6 mpf\|genotype:Tu/hrg1 doulble knockout DKO	GSM2975192	GSM2975192: SplDKO 3; Danio rerio; RNA Seq	GSM2975192		1	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	GEO Accession:GSM2975192	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP131956		SplDKO_3.fastq.gz	fastq	732609543.0	14364893.0	GSM2975192 r1	0:51	A:209020386;C:154988652;G:160405898;T:208183578;N:11029	51	209020386	154988652	160405898	208183578	11029	SRX3638244	SRS2904496	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.88228	0.23609	0.72529	0.50392	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Spleen	Hematopoietic System
47593	47593	SRR6661147	SRX3638243	SRS2904493	SRP131956	PRJNA432507	Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne	GSE109978	Transcriptome Analysis	RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.	pubmed:30248094	SplDKO 2	GSM2975191	source name:whole animal\|tissue:spleen\|age:5 mpf 6 mpf\|genotype:Tu/hrg1 doulble knockout DKO	SplDKO 2	Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.	whole animal	Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	Normal zebrafish husbandary	tissue:spleen\|age:5 mpf 6 mpf\|genotype:Tu/hrg1 doulble knockout DKO	GSM2975191	GSM2975191: SplDKO 2; Danio rerio; RNA Seq	GSM2975191		1	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	GEO Accession:GSM2975191	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP131956		SplDKO_2.fastq.gz	fastq	747985635.0	14666385.0	GSM2975191 r1	0:51	A:209892939;C:160527969;G:165683955;T:211869190;N:11582	51	209892939	160527969	165683955	211869190	11582	SRX3638243	SRS2904493	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.90267	0.20054	0.7249	0.53668	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Spleen	Hematopoietic System
47594	47594	SRR6661146	SRX3638242	SRS2904494	SRP131956	PRJNA432507	Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne	GSE109978	Transcriptome Analysis	RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.	pubmed:30248094	SplDKO 1	GSM2975190	source name:whole animal\|tissue:spleen\|age:5 mpf 6 mpf\|genotype:Tu/hrg1 doulble knockout DKO	SplDKO 1	Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87.	whole animal	Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	Normal zebrafish husbandary	tissue:spleen\|age:5 mpf 6 mpf\|genotype:Tu/hrg1 doulble knockout DKO	GSM2975190	GSM2975190: SplDKO 1; Danio rerio; RNA Seq	GSM2975190		1	TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation	GEO Accession:GSM2975190	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP131956		SplDKO_1.fastq.gz	fastq	724574391.0	14207341.0	GSM2975190 r1	0:51	A:207549130;C:151913145;G:156789401;T:208311727;N:10988	51	207549130	151913145	156789401	208311727	10988	SRX3638242	SRS2904494	SRA654641	GEO	Laboratory of Molecular Biology, NIH/NIDDK	1	0.89742	0.2275	0.71547	0.5072	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2018-02-01	Adult	Adult	Spleen	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");;