metadata: run_metadata: 73 rows where experiment.library_layout = "SINGLE", technology = "smartseq" and tissue

73 rows where experiment.library_layout = "SINGLE", technology = "smartseq" and tissue_curation = "Blood"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.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
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
51262	51262	SRR8632323	SRX5431024	SRS4411019	SRP186864	PRJNA524286	The miR 199 CDK2 axis modulates neutrophil migration and systemic inflammation	GSE127174	Transcriptome Analysis	We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils and RNAseq for identification of mRNA targets of miRNA 199 in neutrophils Overall design: for miRNA profiles we compared the miRNA present in zebrafish neutrophils and keratinocytes to the whole embryo. for miR 199 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR199 or vector control	pubmed:31451657	lyzC+	GSM3629718	source name:neutrophils\|strain background:AB\|gentoype/variation:wild type\|tissue:neutrophils	lyzC+	Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000 for Samples 6 11. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter: for Samples 1 5: “ alignEndsType EndToEnd outFilterMismatchNmax 1 outFilterMultimapScoreRange 0 outFilterMultimapNmax 10 outSAMunmapped Within outFilterScoreMinOverLread 0 outFilterMatchNminOverLread 0 outFilterMatchNmin 16 alignSJDBoverhangMin 1000” for Samples 6 11: “ outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5: “ s 1 –Q 10” for Samples 6 11 " p Q 10". The data was filtered: for Samples 1 5 using read count > 10 in more than 1 of the samples; for Samples 6 11 using read count per million CPM > 0.5 in more than 3 of the samples normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts	neutrophils	transgenic zebrafish lines were used to produce embryos. For miRNA profiling transgenic lines expressing GFP in either neutrophils or apical keratincyes were used. For miR 199 target discovery transgenic lines expressing miR 199 or a vector control together with a GFP reporter were used.	tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..	zebrafish embryos were grown to 3 dpf in embryonic media	strain background:AB\|gentoype/variation:wild type\|tissue:neutrophils	GSM3629718	GSM3629718: lyzC+; Danio rerio; RNA Seq	GSM3629718		1	tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..	GEO Accession:GSM3629718	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP186864		lyzc.fastq.gz	fastq	98774200.0	1975484.0	GSM3629718 r1	0:50	A:18442541;C:23267011;G:29755652;T:27302395;N:6601	50	18442541	23267011	29755652	27302395	6601	SRX5431024	SRS4411019	SRA852308	GEO	Department of Biological Sciences, Purdue University	1	0.24185	0.03969	0.94708	0.65078	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	trueseq	sc	single_cell_plate	smartseq	United States	2019-02-26	Larval	Larval	Blood	Hematopoietic System
71860	71860	SRR22135238	SRX18114786	SRS15617125	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	D Emergency granulopoiesis neutrophils post infection rep 4	GSM6704384	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	D Emergency granulopoiesis neutrophils post infection rep 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	GSM6704384	GSM6704384: D Emergency granulopoiesis neutrophils post infection rep 4; Danio rerio; RNA Seq	GSM6704384 r1	GSM6704384	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	D4_S16_L001_R1_001.fastq.gz	fastq	492998897.0	6538726.0	GSM6704384 r1	0:75.40	A:142208659;C:103614806;G:105979666;T:141151718;N:44048	75	142208659	103614806	105979666	141151718	44048	SRX18114786	SRS15617125	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90296	0.31723	0.76771	0.48693	75	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71861	71861	SRR22135239	SRX18114786	SRS15617125	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	D Emergency granulopoiesis neutrophils post infection rep 4	GSM6704384	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	D Emergency granulopoiesis neutrophils post infection rep 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	GSM6704384	GSM6704384: D Emergency granulopoiesis neutrophils post infection rep 4; Danio rerio; RNA Seq	GSM6704384 r1	GSM6704384	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	D4_S16_L002_R1_001.fastq.gz	fastq	486522568.0	6452453.0	GSM6704384 r2	0:75.40	A:140379916;C:102147805;G:104621474;T:139332047;N:41326	75	140379916	102147805	104621474	139332047	41326	SRX18114786	SRS15617125	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.9012	0.31652	0.7681	0.48379	75	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71862	71862	SRR22135240	SRX18114786	SRS15617125	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	D Emergency granulopoiesis neutrophils post infection rep 4	GSM6704384	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	D Emergency granulopoiesis neutrophils post infection rep 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	GSM6704384	GSM6704384: D Emergency granulopoiesis neutrophils post infection rep 4; Danio rerio; RNA Seq	GSM6704384 r1	GSM6704384	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	D4_S16_L003_R1_001.fastq.gz	fastq	499411895.0	6623685.0	GSM6704384 r3	0:75.40	A:144028426;C:105024209;G:107425776;T:142887718;N:45766	75	144028426	105024209	107425776	142887718	45766	SRX18114786	SRS15617125	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90214	0.3188	0.76863	0.48665	75	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71863	71863	SRR22135241	SRX18114786	SRS15617125	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	D Emergency granulopoiesis neutrophils post infection rep 4	GSM6704384	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	D Emergency granulopoiesis neutrophils post infection rep 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	GSM6704384	GSM6704384: D Emergency granulopoiesis neutrophils post infection rep 4; Danio rerio; RNA Seq	GSM6704384 r1	GSM6704384	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	D4_S16_L004_R1_001.fastq.gz	fastq	491985584.0	6524636.0	GSM6704384 r4	0:75.40	A:142093034;C:103222008;G:105595618;T:141031132;N:43792	75	142093034	103222008	105595618	141031132	43792	SRX18114786	SRS15617125	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90151	0.31805	0.7682	0.48804	75	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71864	71864	SRR22135242	SRX18114785	SRS15617124	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	D Emergency granulopoiesis neutrophils post infection rep 3	GSM6704383	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	D Emergency granulopoiesis neutrophils post infection rep 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	GSM6704383	GSM6704383: D Emergency granulopoiesis neutrophils post infection rep 3; Danio rerio; RNA Seq	GSM6704383 r1	GSM6704383	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	D3_S15_L001_R1_001.fastq.gz	fastq	501524165.0	6667267.0	GSM6704383 r1	0:75.22	A:143118995;C:106791152;G:109715789;T:141789029;N:109200	75	143118995	106791152	109715789	141789029	109200	SRX18114785	SRS15617124	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90211	0.3184	0.7569	0.48864	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71865	71865	SRR22135243	SRX18114785	SRS15617124	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	D Emergency granulopoiesis neutrophils post infection rep 3	GSM6704383	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	D Emergency granulopoiesis neutrophils post infection rep 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	GSM6704383	GSM6704383: D Emergency granulopoiesis neutrophils post infection rep 3; Danio rerio; RNA Seq	GSM6704383 r1	GSM6704383	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	D3_S15_L002_R1_001.fastq.gz	fastq	494015859.0	6567071.0	GSM6704383 r2	0:75.23	A:140996216;C:105164019;G:108107082;T:139639536;N:109006	75	140996216	105164019	108107082	139639536	109006	SRX18114785	SRS15617124	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90121	0.31746	0.75883	0.47681	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71866	71866	SRR22135244	SRX18114785	SRS15617124	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	D Emergency granulopoiesis neutrophils post infection rep 3	GSM6704383	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	D Emergency granulopoiesis neutrophils post infection rep 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	GSM6704383	GSM6704383: D Emergency granulopoiesis neutrophils post infection rep 3; Danio rerio; RNA Seq	GSM6704383 r1	GSM6704383	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	D3_S15_L003_R1_001.fastq.gz	fastq	508620356.0	6761277.0	GSM6704383 r3	0:75.23	A:145208025;C:108358330;G:111248753;T:143692334;N:112914	75	145208025	108358330	111248753	143692334	112914	SRX18114785	SRS15617124	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90315	0.32027	0.7582	0.49103	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71867	71867	SRR22135245	SRX18114785	SRS15617124	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	D Emergency granulopoiesis neutrophils post infection rep 3	GSM6704383	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	D Emergency granulopoiesis neutrophils post infection rep 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	GSM6704383	GSM6704383: D Emergency granulopoiesis neutrophils post infection rep 3; Danio rerio; RNA Seq	GSM6704383 r1	GSM6704383	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	D3_S15_L004_R1_001.fastq.gz	fastq	502842850.0	6684188.0	GSM6704383 r4	0:75.23	A:143669043;C:106987130;G:109853730;T:142224644;N:108303	75	143669043	106987130	109853730	142224644	108303	SRX18114785	SRS15617124	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90348	0.31941	0.75941	0.47942	75	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71868	71868	SRR22135246	SRX18114784	SRS15617123	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	D Emergency granulopoiesis neutrophils post infection rep 2	GSM6704382	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	D Emergency granulopoiesis neutrophils post infection rep 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	GSM6704382	GSM6704382: D Emergency granulopoiesis neutrophils post infection rep 2; Danio rerio; RNA Seq	GSM6704382 r1	GSM6704382	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	D2_S14_L001_R1_001.fastq.gz	fastq	623282435.0	8275237.0	GSM6704382 r1	0:75.32	A:174770372;C:136305753;G:139952685;T:172170159;N:83466	75	174770372	136305753	139952685	172170159	83466	SRX18114784	SRS15617123	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.91734	0.22049	0.77981	0.48624	75	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71869	71869	SRR22135247	SRX18114784	SRS15617123	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	D Emergency granulopoiesis neutrophils post infection rep 2	GSM6704382	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	D Emergency granulopoiesis neutrophils post infection rep 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	GSM6704382	GSM6704382: D Emergency granulopoiesis neutrophils post infection rep 2; Danio rerio; RNA Seq	GSM6704382 r1	GSM6704382	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	D2_S14_L002_R1_001.fastq.gz	fastq	614630529.0	8159803.0	GSM6704382 r2	0:75.32	A:172330413;C:134368821;G:138082642;T:169768983;N:79670	75	172330413	134368821	138082642	169768983	79670	SRX18114784	SRS15617123	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.91718	0.22076	0.78216	0.48999	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71870	71870	SRR22135248	SRX18114784	SRS15617123	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	D Emergency granulopoiesis neutrophils post infection rep 2	GSM6704382	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	D Emergency granulopoiesis neutrophils post infection rep 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	GSM6704382	GSM6704382: D Emergency granulopoiesis neutrophils post infection rep 2; Danio rerio; RNA Seq	GSM6704382 r1	GSM6704382	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	D2_S14_L003_R1_001.fastq.gz	fastq	632075043.0	8391673.0	GSM6704382 r3	0:75.32	A:177241582;C:138262538;G:141930731;T:174553877;N:86315	75	177241582	138262538	141930731	174553877	86315	SRX18114784	SRS15617123	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.91775	0.22141	0.78125	0.48963	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71871	71871	SRR22135249	SRX18114784	SRS15617123	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	D Emergency granulopoiesis neutrophils post infection rep 2	GSM6704382	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	D Emergency granulopoiesis neutrophils post infection rep 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	GSM6704382	GSM6704382: D Emergency granulopoiesis neutrophils post infection rep 2; Danio rerio; RNA Seq	GSM6704382 r1	GSM6704382	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	D2_S14_L004_R1_001.fastq.gz	fastq	626788952.0	8320830.0	GSM6704382 r4	0:75.33	A:175855705;C:136981154;G:140605741;T:173263179;N:83173	75	175855705	136981154	140605741	173263179	83173	SRX18114784	SRS15617123	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.91555	0.22131	0.78021	0.48958	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71872	71872	SRR22135250	SRX18114783	SRS15617122	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	D Emergency granulopoiesis neutrophils post infection rep 1	GSM6704381	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	D Emergency granulopoiesis neutrophils post infection rep 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	GSM6704381	GSM6704381: D Emergency granulopoiesis neutrophils post infection rep 1; Danio rerio; RNA Seq	GSM6704381 r1	GSM6704381	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	D1_S13_L001_R1_001.fastq.gz	fastq	600629404.0	7963900.0	GSM6704381 r1	0:75.42	A:173903456;C:125449559;G:128569714;T:172648882;N:57793	75	173903456	125449559	128569714	172648882	57793	SRX18114783	SRS15617122	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90278	0.30767	0.77122	0.47302	75	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71873	71873	SRR22135251	SRX18114783	SRS15617122	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	D Emergency granulopoiesis neutrophils post infection rep 1	GSM6704381	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	D Emergency granulopoiesis neutrophils post infection rep 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	GSM6704381	GSM6704381: D Emergency granulopoiesis neutrophils post infection rep 1; Danio rerio; RNA Seq	GSM6704381 r1	GSM6704381	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	D1_S13_L002_R1_001.fastq.gz	fastq	593575447.0	7870109.0	GSM6704381 r2	0:75.42	A:171856506;C:123898037;G:127183143;T:170577543;N:60218	75	171856506	123898037	127183143	170577543	60218	SRX18114783	SRS15617122	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90213	0.30675	0.77139	0.49143	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71874	71874	SRR22135252	SRX18114783	SRS15617122	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	D Emergency granulopoiesis neutrophils post infection rep 1	GSM6704381	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	D Emergency granulopoiesis neutrophils post infection rep 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	GSM6704381	GSM6704381: D Emergency granulopoiesis neutrophils post infection rep 1; Danio rerio; RNA Seq	GSM6704381 r1	GSM6704381	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	D1_S13_L003_R1_001.fastq.gz	fastq	607759183.0	8058183.0	GSM6704381 r3	0:75.42	A:175961893;C:126968252;G:130145843;T:174622136;N:61059	75	175961893	126968252	130145843	174622136	61059	SRX18114783	SRS15617122	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90286	0.3077	0.77536	0.48168	75	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71875	71875	SRR22135253	SRX18114783	SRS15617122	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	D Emergency granulopoiesis neutrophils post infection rep 1	GSM6704381	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	D Emergency granulopoiesis neutrophils post infection rep 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infection	GSM6704381	GSM6704381: D Emergency granulopoiesis neutrophils post infection rep 1; Danio rerio; RNA Seq	GSM6704381 r1	GSM6704381	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	D1_S13_L004_R1_001.fastq.gz	fastq	603840714.0	8006177.0	GSM6704381 r4	0:75.42	A:174992048;C:125976469;G:129096065;T:173715134;N:60998	75	174992048	125976469	129096065	173715134	60998	SRX18114783	SRS15617122	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90246	0.30756	0.77376	0.49091	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71876	71876	SRR22135254	SRX18114782	SRS15617121	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	C Emergency granulopoiesis neutrophils before infection rep 4	GSM6704380	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	C Emergency granulopoiesis neutrophils before infection rep 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704380	GSM6704380: C Emergency granulopoiesis neutrophils before infection rep 4; Danio rerio; RNA Seq	GSM6704380 r1	GSM6704380	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	C4_S12_L001_R1_001.fastq.gz	fastq	508969256.0	6764957.0	GSM6704380 r1	0:75.24	A:141573006;C:112320231;G:115240302;T:139729984;N:105733	75	141573006	112320231	115240302	139729984	105733	SRX18114782	SRS15617121	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.91769	0.18294	0.79022	0.45268	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71877	71877	SRR22135255	SRX18114782	SRS15617121	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	C Emergency granulopoiesis neutrophils before infection rep 4	GSM6704380	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	C Emergency granulopoiesis neutrophils before infection rep 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704380	GSM6704380: C Emergency granulopoiesis neutrophils before infection rep 4; Danio rerio; RNA Seq	GSM6704380 r1	GSM6704380	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	C4_S12_L002_R1_001.fastq.gz	fastq	497898449.0	6617513.0	GSM6704380 r2	0:75.24	A:138484840;C:109817035;G:112807273;T:136689722;N:99579	75	138484840	109817035	112807273	136689722	99579	SRX18114782	SRS15617121	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.91685	0.18325	0.79097	0.45681	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71878	71878	SRR22135256	SRX18114782	SRS15617121	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	C Emergency granulopoiesis neutrophils before infection rep 4	GSM6704380	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	C Emergency granulopoiesis neutrophils before infection rep 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704380	GSM6704380: C Emergency granulopoiesis neutrophils before infection rep 4; Danio rerio; RNA Seq	GSM6704380 r1	GSM6704380	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	C4_S12_L003_R1_001.fastq.gz	fastq	507294699.0	6742347.0	GSM6704380 r3	0:75.24	A:141086540;C:111970071;G:114847428;T:139285500;N:105160	75	141086540	111970071	114847428	139285500	105160	SRX18114782	SRS15617121	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.91678	0.18312	0.79005	0.45106	39	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71879	71879	SRR22135257	SRX18114782	SRS15617121	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	C Emergency granulopoiesis neutrophils before infection rep 4	GSM6704380	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	C Emergency granulopoiesis neutrophils before infection rep 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704380	GSM6704380: C Emergency granulopoiesis neutrophils before infection rep 4; Danio rerio; RNA Seq	GSM6704380 r1	GSM6704380	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	C4_S12_L004_R1_001.fastq.gz	fastq	506020854.0	6725110.0	GSM6704380 r4	0:75.24	A:140855644;C:111555468;G:114417168;T:139090690;N:101884	75	140855644	111555468	114417168	139090690	101884	SRX18114782	SRS15617121	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.9177	0.18523	0.79044	0.45269	75	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71880	71880	SRR22135258	SRX18114781	SRS15617120	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	C Emergency granulopoiesis neutrophils before infection rep 3	GSM6704379	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	C Emergency granulopoiesis neutrophils before infection rep 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704379	GSM6704379: C Emergency granulopoiesis neutrophils before infection rep 3; Danio rerio; RNA Seq	GSM6704379 r1	GSM6704379	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	C3_S11_L001_R1_001.fastq.gz	fastq	515541266.0	6855812.0	GSM6704379 r1	0:75.20	A:144554779;C:112398878;G:115543169;T:142918279;N:126161	75	144554779	112398878	115543169	142918279	126161	SRX18114781	SRS15617120	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90004	0.21641	0.78319	0.4509	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71881	71881	SRR22135259	SRX18114781	SRS15617120	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	C Emergency granulopoiesis neutrophils before infection rep 3	GSM6704379	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	C Emergency granulopoiesis neutrophils before infection rep 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704379	GSM6704379: C Emergency granulopoiesis neutrophils before infection rep 3; Danio rerio; RNA Seq	GSM6704379 r1	GSM6704379	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	C3_S11_L002_R1_001.fastq.gz	fastq	503385097.0	6693566.0	GSM6704379 r2	0:75.20	A:141115462;C:109707827;G:112901695;T:139545873;N:114240	75	141115462	109707827	112901695	139545873	114240	SRX18114781	SRS15617120	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.89994	0.21764	0.78439	0.45429	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71882	71882	SRR22135260	SRX18114781	SRS15617120	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	C Emergency granulopoiesis neutrophils before infection rep 3	GSM6704379	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	C Emergency granulopoiesis neutrophils before infection rep 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704379	GSM6704379: C Emergency granulopoiesis neutrophils before infection rep 3; Danio rerio; RNA Seq	GSM6704379 r1	GSM6704379	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	C3_S11_L003_R1_001.fastq.gz	fastq	514809631.0	6845860.0	GSM6704379 r3	0:75.20	A:144414867;C:112234002;G:115354218;T:142684425;N:122119	75	144414867	112234002	115354218	142684425	122119	SRX18114781	SRS15617120	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90029	0.21717	0.78543	0.45288	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71883	71883	SRR22135261	SRX18114781	SRS15617120	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	C Emergency granulopoiesis neutrophils before infection rep 3	GSM6704379	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	C Emergency granulopoiesis neutrophils before infection rep 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704379	GSM6704379: C Emergency granulopoiesis neutrophils before infection rep 3; Danio rerio; RNA Seq	GSM6704379 r1	GSM6704379	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	C3_S11_L004_R1_001.fastq.gz	fastq	511959662.0	6807750.0	GSM6704379 r4	0:75.20	A:143660849;C:111541802;G:114619614;T:142010084;N:127313	75	143660849	111541802	114619614	142010084	127313	SRX18114781	SRS15617120	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90154	0.21666	0.78409	0.44479	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71884	71884	SRR22135262	SRX18114780	SRS15617119	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	C Emergency granulopoiesis neutrophils before infection rep 2	GSM6704378	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	C Emergency granulopoiesis neutrophils before infection rep 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704378	GSM6704378: C Emergency granulopoiesis neutrophils before infection rep 2; Danio rerio; RNA Seq	GSM6704378 r1	GSM6704378	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	C2_S10_L001_R1_001.fastq.gz	fastq	552657716.0	7351840.0	GSM6704378 r1	0:75.17	A:154321273;C:121108427;G:124253085;T:152829634;N:145297	75	154321273	121108427	124253085	152829634	145297	SRX18114780	SRS15617119	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90595	0.21524	0.78727	0.44305	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71885	71885	SRR22135263	SRX18114780	SRS15617119	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	C Emergency granulopoiesis neutrophils before infection rep 2	GSM6704378	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	C Emergency granulopoiesis neutrophils before infection rep 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704378	GSM6704378: C Emergency granulopoiesis neutrophils before infection rep 2; Danio rerio; RNA Seq	GSM6704378 r1	GSM6704378	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	C2_S10_L002_R1_001.fastq.gz	fastq	541084407.0	7197405.0	GSM6704378 r2	0:75.18	A:151110182;C:118494427;G:121734523;T:149606835;N:138440	75	151110182	118494427	121734523	149606835	138440	SRX18114780	SRS15617119	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90451	0.21355	0.7864	0.46217	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71886	71886	SRR22135264	SRX18114780	SRS15617119	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	C Emergency granulopoiesis neutrophils before infection rep 2	GSM6704378	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	C Emergency granulopoiesis neutrophils before infection rep 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704378	GSM6704378: C Emergency granulopoiesis neutrophils before infection rep 2; Danio rerio; RNA Seq	GSM6704378 r1	GSM6704378	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	C2_S10_L003_R1_001.fastq.gz	fastq	552243490.0	7345866.0	GSM6704378 r3	0:75.18	A:154273133;C:121031449;G:124104784;T:152689350;N:144774	75	154273133	121031449	124104784	152689350	144774	SRX18114780	SRS15617119	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90328	0.21377	0.78794	0.46314	74	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71887	71887	SRR22135265	SRX18114780	SRS15617119	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	C Emergency granulopoiesis neutrophils before infection rep 2	GSM6704378	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	C Emergency granulopoiesis neutrophils before infection rep 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704378	GSM6704378: C Emergency granulopoiesis neutrophils before infection rep 2; Danio rerio; RNA Seq	GSM6704378 r1	GSM6704378	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	C2_S10_L004_R1_001.fastq.gz	fastq	550045892.0	7316300.0	GSM6704378 r4	0:75.18	A:153756888;C:120418987;G:123493369;T:152233493;N:143155	75	153756888	120418987	123493369	152233493	143155	SRX18114780	SRS15617119	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90607	0.21521	0.78884	0.4602	75	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71888	71888	SRR22135266	SRX18114779	SRS15617118	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	C Emergency granulopoiesis neutrophils before infection rep 1	GSM6704377	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	C Emergency granulopoiesis neutrophils before infection rep 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704377	GSM6704377: C Emergency granulopoiesis neutrophils before infection rep 1; Danio rerio; RNA Seq	GSM6704377 r1	GSM6704377	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	C1_S9_L001_R1_001.fastq.gz	fastq	447668353.0	5946872.0	GSM6704377 r1	0:75.28	A:126591403;C:96173272;G:98995296;T:125821091;N:87291	75	126591403	96173272	98995296	125821091	87291	SRX18114779	SRS15617118	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.9068	0.19712	0.78403	0.44792	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71889	71889	SRR22135267	SRX18114779	SRS15617118	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	C Emergency granulopoiesis neutrophils before infection rep 1	GSM6704377	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	C Emergency granulopoiesis neutrophils before infection rep 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704377	GSM6704377: C Emergency granulopoiesis neutrophils before infection rep 1; Danio rerio; RNA Seq	GSM6704377 r1	GSM6704377	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	C1_S9_L002_R1_001.fastq.gz	fastq	438741991.0	5827957.0	GSM6704377 r2	0:75.28	A:124052360;C:94187980;G:97086359;T:123328717;N:86575	75	124052360	94187980	97086359	123328717	86575	SRX18114779	SRS15617118	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90575	0.19469	0.78372	0.44497	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71890	71890	SRR22135268	SRX18114779	SRS15617118	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	C Emergency granulopoiesis neutrophils before infection rep 1	GSM6704377	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	C Emergency granulopoiesis neutrophils before infection rep 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704377	GSM6704377: C Emergency granulopoiesis neutrophils before infection rep 1; Danio rerio; RNA Seq	GSM6704377 r1	GSM6704377	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	C1_S9_L003_R1_001.fastq.gz	fastq	445278983.0	5914944.0	GSM6704377 r3	0:75.28	A:125938011;C:95660137;G:98439497;T:125152218;N:89120	75	125938011	95660137	98439497	125152218	89120	SRX18114779	SRS15617118	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90509	0.19724	0.78368	0.44808	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71891	71891	SRR22135269	SRX18114779	SRS15617118	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	C Emergency granulopoiesis neutrophils before infection rep 1	GSM6704377	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	C Emergency granulopoiesis neutrophils before infection rep 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704377	GSM6704377: C Emergency granulopoiesis neutrophils before infection rep 1; Danio rerio; RNA Seq	GSM6704377 r1	GSM6704377	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	C1_S9_L004_R1_001.fastq.gz	fastq	445891044.0	5922741.0	GSM6704377 r4	0:75.28	A:126199901;C:95673429;G:98452672;T:125477132;N:87910	75	126199901	95673429	98452672	125477132	87910	SRX18114779	SRS15617118	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90585	0.19754	0.78599	0.44544	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71892	71892	SRR22135270	SRX18114778	SRS15617117	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	B Steady state neutrophils post infection rep 4	GSM6704376	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	B Steady state neutrophils post infection rep 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	GSM6704376	GSM6704376: B Steady state neutrophils post infection rep 4; Danio rerio; RNA Seq	GSM6704376 r1	GSM6704376	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	B4_S8_L001_R1_001.fastq.gz	fastq	574532012.0	7627510.0	GSM6704376 r1	0:75.32	A:163780397;C:122304319;G:125503282;T:162857913;N:86101	75	163780397	122304319	125503282	162857913	86101	SRX18114778	SRS15617117	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90532	0.25104	0.80904	0.49523	75	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71893	71893	SRR22135271	SRX18114778	SRS15617117	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	B Steady state neutrophils post infection rep 4	GSM6704376	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	B Steady state neutrophils post infection rep 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	GSM6704376	GSM6704376: B Steady state neutrophils post infection rep 4; Danio rerio; RNA Seq	GSM6704376 r1	GSM6704376	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	B4_S8_L002_R1_001.fastq.gz	fastq	567091661.0	7528335.0	GSM6704376 r2	0:75.33	A:161676443;C:120637867;G:123939259;T:160748764;N:89328	75	161676443	120637867	123939259	160748764	89328	SRX18114778	SRS15617117	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.9036	0.25306	0.81195	0.4996	75	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71894	71894	SRR22135272	SRX18114778	SRS15617117	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	B Steady state neutrophils post infection rep 4	GSM6704376	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	B Steady state neutrophils post infection rep 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	GSM6704376	GSM6704376: B Steady state neutrophils post infection rep 4; Danio rerio; RNA Seq	GSM6704376 r1	GSM6704376	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	B4_S8_L003_R1_001.fastq.gz	fastq	582558189.0	7733624.0	GSM6704376 r3	0:75.33	A:166076160;C:124018499;G:127251962;T:165124826;N:86742	75	166076160	124018499	127251962	165124826	86742	SRX18114778	SRS15617117	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90421	0.25137	0.81152	0.49108	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71895	71895	SRR22135273	SRX18114778	SRS15617117	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	B Steady state neutrophils post infection rep 4	GSM6704376	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	B Steady state neutrophils post infection rep 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	GSM6704376	GSM6704376: B Steady state neutrophils post infection rep 4; Danio rerio; RNA Seq	GSM6704376 r1	GSM6704376	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	B4_S8_L004_R1_001.fastq.gz	fastq	578785396.0	7683199.0	GSM6704376 r4	0:75.33	A:165147608;C:123102100;G:126311795;T:164136814;N:87079	75	165147608	123102100	126311795	164136814	87079	SRX18114778	SRS15617117	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90474	0.2514	0.80982	0.49658	75	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71896	71896	SRR22135274	SRX18114777	SRS15617116	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	B Steady state neutrophils post infection rep 3	GSM6704375	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	B Steady state neutrophils post infection rep 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	GSM6704375	GSM6704375: B Steady state neutrophils post infection rep 3; Danio rerio; RNA Seq	GSM6704375 r1	GSM6704375	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	B3_S7_L001_R1_001.fastq.gz	fastq	656397994.0	8713988.0	GSM6704375 r1	0:75.33	A:185589925;C:142146818;G:145402800;T:183164174;N:94277	75	185589925	142146818	145402800	183164174	94277	SRX18114777	SRS15617116	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.91171	0.27356	0.78853	0.48819	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71897	71897	SRR22135275	SRX18114777	SRS15617116	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	B Steady state neutrophils post infection rep 3	GSM6704375	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	B Steady state neutrophils post infection rep 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	GSM6704375	GSM6704375: B Steady state neutrophils post infection rep 3; Danio rerio; RNA Seq	GSM6704375 r1	GSM6704375	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	B3_S7_L002_R1_001.fastq.gz	fastq	645590958.0	8569915.0	GSM6704375 r2	0:75.33	A:182559578;C:139709183;G:143118435;T:180110668;N:93094	75	182559578	139709183	143118435	180110668	93094	SRX18114777	SRS15617116	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.91019	0.27463	0.78717	0.47885	74	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71898	71898	SRR22135276	SRX18114777	SRS15617116	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	B Steady state neutrophils post infection rep 3	GSM6704375	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	B Steady state neutrophils post infection rep 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	GSM6704375	GSM6704375: B Steady state neutrophils post infection rep 3; Danio rerio; RNA Seq	GSM6704375 r1	GSM6704375	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	B3_S7_L003_R1_001.fastq.gz	fastq	664553654.0	8821713.0	GSM6704375 r3	0:75.33	A:187896112;C:143953494;G:147220531;T:185386418;N:97099	75	187896112	143953494	147220531	185386418	97099	SRX18114777	SRS15617116	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.91158	0.27367	0.78709	0.4841	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71899	71899	SRR22135277	SRX18114777	SRS15617116	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	B Steady state neutrophils post infection rep 3	GSM6704375	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	B Steady state neutrophils post infection rep 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	GSM6704375	GSM6704375: B Steady state neutrophils post infection rep 3; Danio rerio; RNA Seq	GSM6704375 r1	GSM6704375	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	B3_S7_L004_R1_001.fastq.gz	fastq	657850662.0	8732855.0	GSM6704375 r4	0:75.33	A:186147606;C:142324801;G:145566934;T:183715835;N:95486	75	186147606	142324801	145566934	183715835	95486	SRX18114777	SRS15617116	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.91212	0.27723	0.78867	0.48717	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71900	71900	SRR22135278	SRX18114776	SRS15617115	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	B Steady state neutrophils post infection rep 2	GSM6704374	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	B Steady state neutrophils post infection rep 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	GSM6704374	GSM6704374: B Steady state neutrophils post infection rep 2; Danio rerio; RNA Seq	GSM6704374 r1	GSM6704374	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	B2_S6_L001_R1_001.fastq.gz	fastq	665922182.0	8843583.0	GSM6704374 r1	0:75.30	A:193047705;C:138574676;G:142112492;T:192098499;N:88810	75	193047705	138574676	142112492	192098499	88810	SRX18114776	SRS15617115	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.89936	0.37317	0.76832	0.50617	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71901	71901	SRR22135279	SRX18114776	SRS15617115	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	B Steady state neutrophils post infection rep 2	GSM6704374	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	B Steady state neutrophils post infection rep 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	GSM6704374	GSM6704374: B Steady state neutrophils post infection rep 2; Danio rerio; RNA Seq	GSM6704374 r1	GSM6704374	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	B2_S6_L002_R1_001.fastq.gz	fastq	655881205.0	8709653.0	GSM6704374 r2	0:75.31	A:190170155;C:136425993;G:140040396;T:189155239;N:89422	75	190170155	136425993	140040396	189155239	89422	SRX18114776	SRS15617115	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.89783	0.37312	0.76992	0.50148	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71902	71902	SRR22135280	SRX18114776	SRS15617115	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	B Steady state neutrophils post infection rep 2	GSM6704374	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	B Steady state neutrophils post infection rep 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	GSM6704374	GSM6704374: B Steady state neutrophils post infection rep 2; Danio rerio; RNA Seq	GSM6704374 r1	GSM6704374	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	B2_S6_L003_R1_001.fastq.gz	fastq	675095595.0	8964940.0	GSM6704374 r3	0:75.30	A:195733572;C:140515075;G:144083045;T:194671899;N:92004	75	195733572	140515075	144083045	194671899	92004	SRX18114776	SRS15617115	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.89714	0.37186	0.7696	0.51059	74	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71903	71903	SRR22135281	SRX18114776	SRS15617115	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	B Steady state neutrophils post infection rep 2	GSM6704374	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	B Steady state neutrophils post infection rep 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	GSM6704374	GSM6704374: B Steady state neutrophils post infection rep 2; Danio rerio; RNA Seq	GSM6704374 r1	GSM6704374	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	B2_S6_L004_R1_001.fastq.gz	fastq	671613660.0	8918194.0	GSM6704374 r4	0:75.31	A:194883489;C:139673070;G:143184262;T:193783173;N:89666	75	194883489	139673070	143184262	193783173	89666	SRX18114776	SRS15617115	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.89819	0.37327	0.77009	0.50414	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71904	71904	SRR22135282	SRX18114775	SRS15617114	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	B Steady state neutrophils post infection rep 1	GSM6704373	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	B Steady state neutrophils post infection rep 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	GSM6704373	GSM6704373: B Steady state neutrophils post infection rep 1; Danio rerio; RNA Seq	GSM6704373 r1	GSM6704373	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	B1_S5_L001_R1_001.fastq.gz	fastq	594567346.0	7875162.0	GSM6704373 r1	0:75.50	A:171876573;C:124309648;G:127541058;T:170821373;N:18694	75	171876573	124309648	127541058	170821373	18694	SRX18114775	SRS15617114	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90037	0.32072	0.78285	0.49838	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71905	71905	SRR22135283	SRX18114775	SRS15617114	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	B Steady state neutrophils post infection rep 1	GSM6704373	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	B Steady state neutrophils post infection rep 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	GSM6704373	GSM6704373: B Steady state neutrophils post infection rep 1; Danio rerio; RNA Seq	GSM6704373 r1	GSM6704373	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	B1_S5_L002_R1_001.fastq.gz	fastq	586924658.0	7773886.0	GSM6704373 r2	0:75.50	A:169696313;C:122638495;G:125948883;T:168622123;N:18844	75	169696313	122638495	125948883	168622123	18844	SRX18114775	SRS15617114	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.89911	0.32047	0.78257	0.48981	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71906	71906	SRR22135284	SRX18114775	SRS15617114	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	B Steady state neutrophils post infection rep 1	GSM6704373	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	B Steady state neutrophils post infection rep 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	GSM6704373	GSM6704373: B Steady state neutrophils post infection rep 1; Danio rerio; RNA Seq	GSM6704373 r1	GSM6704373	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	B1_S5_L003_R1_001.fastq.gz	fastq	602045323.0	7974129.0	GSM6704373 r3	0:75.50	A:174025822;C:125889064;G:129169226;T:172939952;N:21259	75	174025822	125889064	129169226	172939952	21259	SRX18114775	SRS15617114	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.9004	0.3187	0.78218	0.48865	75	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71907	71907	SRR22135285	SRX18114775	SRS15617114	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	B Steady state neutrophils post infection rep 1	GSM6704373	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	B Steady state neutrophils post infection rep 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:post infecton	GSM6704373	GSM6704373: B Steady state neutrophils post infection rep 1; Danio rerio; RNA Seq	GSM6704373 r1	GSM6704373	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	B1_S5_L004_R1_001.fastq.gz	fastq	598770801.0	7930776.0	GSM6704373 r4	0:75.50	A:173211820;C:125089438;G:128295783;T:172152732;N:21028	75	173211820	125089438	128295783	172152732	21028	SRX18114775	SRS15617114	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.8998	0.32049	0.78628	0.49551	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71908	71908	SRR22135286	SRX18114774	SRS15617112	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	A Steady state neutrophils before infection rep 4	GSM6704372	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	A Steady state neutrophils before infection rep 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704372	GSM6704372: A Steady state neutrophils before infection rep 4; Danio rerio; RNA Seq	GSM6704372 r1	GSM6704372	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	A4_S4_L001_R1_001.fastq.gz	fastq	621198094.0	8258867.0	GSM6704372 r1	0:75.22	A:176643966;C:132813551;G:136334689;T:175255713;N:150175	75	176643966	132813551	136334689	175255713	150175	SRX18114774	SRS15617112	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90761	0.30597	0.75485	0.45365	75	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71909	71909	SRR22135287	SRX18114774	SRS15617112	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	A Steady state neutrophils before infection rep 4	GSM6704372	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	A Steady state neutrophils before infection rep 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704372	GSM6704372: A Steady state neutrophils before infection rep 4; Danio rerio; RNA Seq	GSM6704372 r1	GSM6704372	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	A4_S4_L002_R1_001.fastq.gz	fastq	611954607.0	8135473.0	GSM6704372 r2	0:75.22	A:174000698;C:130804474;G:134435770;T:172566404;N:147261	75	174000698	130804474	134435770	172566404	147261	SRX18114774	SRS15617112	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90501	0.30184	0.75631	0.46282	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71910	71910	SRR22135288	SRX18114774	SRS15617112	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	A Steady state neutrophils before infection rep 4	GSM6704372	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	A Steady state neutrophils before infection rep 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704372	GSM6704372: A Steady state neutrophils before infection rep 4; Danio rerio; RNA Seq	GSM6704372 r1	GSM6704372	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	A4_S4_L003_R1_001.fastq.gz	fastq	629500245.0	8368905.0	GSM6704372 r3	0:75.22	A:179021916;C:134627504;G:138210108;T:177486500;N:154217	75	179021916	134627504	138210108	177486500	154217	SRX18114774	SRS15617112	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90589	0.30523	0.75388	0.45673	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71911	71911	SRR22135289	SRX18114774	SRS15617112	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	A Steady state neutrophils before infection rep 4	GSM6704372	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	A Steady state neutrophils before infection rep 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704372	GSM6704372: A Steady state neutrophils before infection rep 4; Danio rerio; RNA Seq	GSM6704372 r1	GSM6704372	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	A4_S4_L004_R1_001.fastq.gz	fastq	625379947.0	8314073.0	GSM6704372 r4	0:75.22	A:177971698;C:133602455;G:137146838;T:176505556;N:153400	75	177971698	133602455	137146838	176505556	153400	SRX18114774	SRS15617112	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90589	0.30348	0.75536	0.46815	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71912	71912	SRR22135290	SRX18114773	SRS15617113	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	A Steady state neutrophils before infection rep 3	GSM6704371	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	A Steady state neutrophils before infection rep 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704371	GSM6704371: A Steady state neutrophils before infection rep 3; Danio rerio; RNA Seq	GSM6704371 r1	GSM6704371	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	A3_S3_L001_R1_001.fastq.gz	fastq	543826599.0	7218345.0	GSM6704371 r1	0:75.34	A:154713832;C:116077145;G:119403989;T:153551527;N:80106	75	154713832	116077145	119403989	153551527	80106	SRX18114773	SRS15617113	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90642	0.27162	0.76556	0.46405	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71913	71913	SRR22135291	SRX18114773	SRS15617113	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	A Steady state neutrophils before infection rep 3	GSM6704371	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	A Steady state neutrophils before infection rep 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704371	GSM6704371: A Steady state neutrophils before infection rep 3; Danio rerio; RNA Seq	GSM6704371 r1	GSM6704371	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	A3_S3_L002_R1_001.fastq.gz	fastq	535171157.0	7103335.0	GSM6704371 r2	0:75.34	A:152294007;C:114137191;G:117552563;T:151108712;N:78684	75	152294007	114137191	117552563	151108712	78684	SRX18114773	SRS15617113	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90489	0.27324	0.76439	0.46199	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71914	71914	SRR22135292	SRX18114773	SRS15617113	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	A Steady state neutrophils before infection rep 3	GSM6704371	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	A Steady state neutrophils before infection rep 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704371	GSM6704371: A Steady state neutrophils before infection rep 3; Danio rerio; RNA Seq	GSM6704371 r1	GSM6704371	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	A3_S3_L003_R1_001.fastq.gz	fastq	550683289.0	7309288.0	GSM6704371 r3	0:75.34	A:156729411;C:117515485;G:120894282;T:155460425;N:83686	75	156729411	117515485	120894282	155460425	83686	SRX18114773	SRS15617113	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90606	0.27336	0.76504	0.4637	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71915	71915	SRR22135293	SRX18114773	SRS15617113	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	A Steady state neutrophils before infection rep 3	GSM6704371	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	A Steady state neutrophils before infection rep 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704371	GSM6704371: A Steady state neutrophils before infection rep 3; Danio rerio; RNA Seq	GSM6704371 r1	GSM6704371	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	A3_S3_L004_R1_001.fastq.gz	fastq	545377006.0	7238493.0	GSM6704371 r4	0:75.34	A:155295590;C:116299389;G:119572738;T:154129682;N:79607	75	155295590	116299389	119572738	154129682	79607	SRX18114773	SRS15617113	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90456	0.27376	0.7654	0.46511	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71916	71916	SRR22135294	SRX18114772	SRS15617110	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	A Steady state neutrophils before infection rep 2	GSM6704370	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	A Steady state neutrophils before infection rep 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704370	GSM6704370: A Steady state neutrophils before infection rep 2; Danio rerio; RNA Seq	GSM6704370 r1	GSM6704370	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	A2_S2_L001_R1_001.fastq.gz	fastq	626577914.0	8324976.0	GSM6704370 r1	0:75.26	A:177527002;C:134434391;G:138069216;T:176421125;N:126180	75	177527002	134434391	138069216	176421125	126180	SRX18114772	SRS15617110	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90657	0.25226	0.76469	0.4664	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71917	71917	SRR22135295	SRX18114772	SRS15617110	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	A Steady state neutrophils before infection rep 2	GSM6704370	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	A Steady state neutrophils before infection rep 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704370	GSM6704370: A Steady state neutrophils before infection rep 2; Danio rerio; RNA Seq	GSM6704370 r1	GSM6704370	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	A2_S2_L002_R1_001.fastq.gz	fastq	617578633.0	8204870.0	GSM6704370 r2	0:75.27	A:174988622;C:132463183;G:136167568;T:173836269;N:122991	75	174988622	132463183	136167568	173836269	122991	SRX18114772	SRS15617110	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90726	0.25165	0.7668	0.46386	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71918	71918	SRR22135296	SRX18114772	SRS15617110	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	A Steady state neutrophils before infection rep 2	GSM6704370	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	A Steady state neutrophils before infection rep 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704370	GSM6704370: A Steady state neutrophils before infection rep 2; Danio rerio; RNA Seq	GSM6704370 r1	GSM6704370	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	A2_S2_L003_R1_001.fastq.gz	fastq	635900919.0	8448601.0	GSM6704370 r3	0:75.27	A:180202529;C:136468150;G:140147733;T:178951930;N:130577	75	180202529	136468150	140147733	178951930	130577	SRX18114772	SRS15617110	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90764	0.25375	0.76631	0.46448	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71919	71919	SRR22135297	SRX18114772	SRS15617110	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	A Steady state neutrophils before infection rep 2	GSM6704370	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	A Steady state neutrophils before infection rep 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704370	GSM6704370: A Steady state neutrophils before infection rep 2; Danio rerio; RNA Seq	GSM6704370 r1	GSM6704370	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	A2_S2_L004_R1_001.fastq.gz	fastq	631138590.0	8384630.0	GSM6704370 r4	0:75.27	A:178955692;C:135329025;G:138923290;T:177807419;N:123164	75	178955692	135329025	138923290	177807419	123164	SRX18114772	SRS15617110	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.90764	0.25393	0.76599	0.46605	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71920	71920	SRR22135298	SRX18114771	SRS15617111	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	A Steady state neutrophils before infection rep 1	GSM6704369	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	A Steady state neutrophils before infection rep 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704369	GSM6704369: A Steady state neutrophils before infection rep 1; Danio rerio; RNA Seq	GSM6704369 r1	GSM6704369	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	A1_S1_L001_R1_001.fastq.gz	fastq	666638236.0	8846950.0	GSM6704369 r1	0:75.35	A:192595027;C:139025923;G:143007061;T:191913974;N:96251	75	192595027	139025923	143007061	191913974	96251	SRX18114771	SRS15617111	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.89605	0.34202	0.75523	0.4524	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71921	71921	SRR22135299	SRX18114771	SRS15617111	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	A Steady state neutrophils before infection rep 1	GSM6704369	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	A Steady state neutrophils before infection rep 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704369	GSM6704369: A Steady state neutrophils before infection rep 1; Danio rerio; RNA Seq	GSM6704369 r1	GSM6704369	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	A1_S1_L002_R1_001.fastq.gz	fastq	657847561.0	8729762.0	GSM6704369 r2	0:75.36	A:190090207;C:137097484;G:141180394;T:189392310;N:87166	75	190090207	137097484	141180394	189392310	87166	SRX18114771	SRS15617111	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.89426	0.34013	0.75343	0.46722	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71922	71922	SRR22135300	SRX18114771	SRS15617111	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	A Steady state neutrophils before infection rep 1	GSM6704369	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	A Steady state neutrophils before infection rep 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704369	GSM6704369: A Steady state neutrophils before infection rep 1; Danio rerio; RNA Seq	GSM6704369 r1	GSM6704369	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	A1_S1_L003_R1_001.fastq.gz	fastq	675038173.0	8958002.0	GSM6704369 r3	0:75.36	A:195025040;C:140815603;G:144805513;T:194298995;N:93022	75	195025040	140815603	144805513	194298995	93022	SRX18114771	SRS15617111	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.89368	0.34109	0.75686	0.4643	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System
71923	71923	SRR22135301	SRX18114771	SRS15617111	SRP405741	PRJNA896643	Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils	GSE217064	Transcriptome Analysis	Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.	pubmed:37672586	A Steady state neutrophils before infection rep 1	GSM6704369	tissue:Neutrophil\|cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	A Steady state neutrophils before infection rep 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse 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: GRCz11 Supplementary files format and content: Comma separated value files show FPKM Log2FC and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis	Neutrophil	At 4 dpf neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection or at 3 hours post infection with Salmonella.	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	cell type:Neutrophil\|genotype:Tglyz:DsRED2\|treatment:Before infection	GSM6704369	GSM6704369: A Steady state neutrophils before infection rep 1; Danio rerio; RNA Seq	GSM6704369 r1	GSM6704369	1	Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 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	SRP405741	loader:fastq load.py	A1_S1_L004_R1_001.fastq.gz	fastq	671027513.0	8904690.0	GSM6704369 r4	0:75.36	A:194019724;C:139826315;G:143792562;T:193294415;N:94497	75	194019724	139826315	143792562	193294415	94497	SRX18114771	SRS15617111	SRA1532054	Hall, FMHS, University of Auckland	Hall, FMHS, University of Auckland	1	0.89405	0.3408	0.75511	0.47237	74	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2022-11-01	Larval	Larval	Blood	Hematopoietic System

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