metadata: run_metadata: 527 rows where experiment.library_source = "TRANSCRIPTOMIC" and tissue

527 rows where experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation = "Blood"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
8092	8092	ERR2402432	ERX2443286	ERS2295360	ERP107516	PRJEB25583	The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151	Other	The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 03 14		Hom MO rep3	Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	SAMEA104693977	DPSQ	ENA FIRST PUBLIC:2018 10 12T17:03:15Z\|ENA LAST UPDATE:2018 03 14T19:09:14Z\|External Id:SAMEA104693977\|INSDC center name:DPSQ\|INSDC first public:2018 10 12T17:03:15Z\|INSDC last update:2018 03 14T19:09:14Z\|INSDC status:public\|Submitter Id:CM12\|common name:zebrafish\|sample name:CM12\|scientific name:Danio rerio									NextSeq 500 paired end sequencing	ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 12	unspecified	1		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	NextSeq 500	ERP107516	NextSeq 500 paired end sequencing	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 11 16	CM12.trimmed.read_1.fastq.gz CM12.trimmed.read_2.fastq.gz	fastq fastq	5384061477.0	38388598.0	ena RUN DPSQ 14 03 2018 19:09:09:420 12	0:70.70 1:69.55	A:1490429493;C:1197976503;G:1220014984;T:1475615043;N:25454	70	69	1490429493	1197976503	1220014984	1475615043	25454	ERX2443286	ERS2295360	ERA1246315	European Nucleotide Archive	Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom	2	0.92285	0.9206	0.06862	0.0688	0.73983	0.74566	0.4752	0.49125	76	75	B	B	biological fallback assumption	illumina	nextseq	full_length	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2018-03-14	Undetermined	Embryo	Blood	Hematopoietic System
8093	8093	ERR2402431	ERX2443285	ERS2295359	ERP107516	PRJEB25583	The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151	Other	The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 03 14		Hom MO rep2	Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	SAMEA104693976	DPSQ	ENA FIRST PUBLIC:2018 10 12T17:03:15Z\|ENA LAST UPDATE:2018 03 14T19:09:14Z\|External Id:SAMEA104693976\|INSDC center name:DPSQ\|INSDC first public:2018 10 12T17:03:15Z\|INSDC last update:2018 03 14T19:09:14Z\|INSDC status:public\|Submitter Id:CM11\|common name:zebrafish\|sample name:CM11\|scientific name:Danio rerio									NextSeq 500 paired end sequencing	ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 11	unspecified	1		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	NextSeq 500	ERP107516	NextSeq 500 paired end sequencing	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 11 16	CM11.trimmed.read_1.fastq.gz CM11.trimmed.read_2.fastq.gz	fastq fastq	5472085589.0	38860681.0	ena RUN DPSQ 14 03 2018 19:09:09:420 11	0:70.98 1:69.83	A:1514986213;C:1217661004;G:1240412104;T:1499000816;N:25452	70	69	1514986213	1217661004	1240412104	1499000816	25452	ERX2443285	ERS2295359	ERA1246315	European Nucleotide Archive	Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom	2	0.91987	0.91874	0.0693	0.07042	0.74042	0.74629	0.48229	0.49144	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2018-03-14	Undetermined	Embryo	Blood	Hematopoietic System
8094	8094	ERR2402430	ERX2443284	ERS2295358	ERP107516	PRJEB25583	The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151	Other	The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 03 14		Hom MO rep1	Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	SAMEA104693975	DPSQ	ENA FIRST PUBLIC:2018 10 12T17:03:15Z\|ENA LAST UPDATE:2018 03 14T19:09:14Z\|External Id:SAMEA104693975\|INSDC center name:DPSQ\|INSDC first public:2018 10 12T17:03:15Z\|INSDC last update:2018 03 14T19:09:14Z\|INSDC status:public\|Submitter Id:CM10\|common name:zebrafish\|sample name:CM10\|scientific name:Danio rerio									NextSeq 500 paired end sequencing	ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 10	unspecified	1		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	NextSeq 500	ERP107516	NextSeq 500 paired end sequencing	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 11 16	CM10.trimmed.read_1.fastq.gz CM10.trimmed.read_2.fastq.gz	fastq fastq	6091085806.0	43064771.0	ena RUN DPSQ 14 03 2018 19:09:09:420 10	0:71.33 1:70.11	A:1692450462;C:1348639943;G:1375433963;T:1674532019;N:29419	71	70	1692450462	1348639943	1375433963	1674532019	29419	ERX2443284	ERS2295358	ERA1246315	European Nucleotide Archive	Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom	2	0.92184	0.92064	0.0699	0.0704	0.74286	0.74874	0.48978	0.48997	75	73	B	B	biological fallback assumption	illumina	nextseq	full_length	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2018-03-14	Undetermined	Embryo	Blood	Hematopoietic System
8095	8095	ERR2402429	ERX2443283	ERS2295357	ERP107516	PRJEB25583	The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151	Other	The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 03 14		Hom uninj rep3	Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	SAMEA104693974	DPSQ	ENA FIRST PUBLIC:2018 10 12T17:03:15Z\|ENA LAST UPDATE:2018 03 14T19:09:14Z\|External Id:SAMEA104693974\|INSDC center name:DPSQ\|INSDC first public:2018 10 12T17:03:15Z\|INSDC last update:2018 03 14T19:09:14Z\|INSDC status:public\|Submitter Id:CM9\|common name:zebrafish\|sample name:CM9\|scientific name:Danio rerio									NextSeq 500 paired end sequencing	ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 9	unspecified	1		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	NextSeq 500	ERP107516	NextSeq 500 paired end sequencing	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 11 16	CM9.trimmed.read_1.fastq.gz CM9.trimmed.read_2.fastq.gz	fastq fastq	6329252570.0	45070159.0	ena RUN DPSQ 14 03 2018 19:09:09:420 9	0:70.79 1:69.64	A:1753489708;C:1407193617;G:1433449502;T:1735090181;N:29562	70	69	1753489708	1407193617	1433449502	1735090181	29562	ERX2443283	ERS2295357	ERA1246315	European Nucleotide Archive	Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom	2	0.91683	0.91616	0.06775	0.06825	0.75158	0.75737	0.49386	0.49199	76	75	B	B	biological fallback assumption	illumina	nextseq	full_length	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2018-03-14	Undetermined	Embryo	Blood	Hematopoietic System
8096	8096	ERR2402428	ERX2443282	ERS2295356	ERP107516	PRJEB25583	The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151	Other	The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 03 14		Hom uninj rep2	Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	SAMEA104693973	DPSQ	ENA FIRST PUBLIC:2018 10 12T17:03:15Z\|ENA LAST UPDATE:2018 03 14T19:09:14Z\|External Id:SAMEA104693973\|INSDC center name:DPSQ\|INSDC first public:2018 10 12T17:03:15Z\|INSDC last update:2018 03 14T19:09:14Z\|INSDC status:public\|Submitter Id:CM8\|common name:zebrafish\|sample name:CM8\|scientific name:Danio rerio									NextSeq 500 paired end sequencing	ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 8	unspecified	1		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	NextSeq 500	ERP107516	NextSeq 500 paired end sequencing	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 11 16	CM8.trimmed.read_1.fastq.gz CM8.trimmed.read_2.fastq.gz	fastq fastq	5405185494.0	38637007.0	ena RUN DPSQ 14 03 2018 19:09:09:420 8	0:70.45 1:69.44	A:1491577735;C:1206599147;G:1229354248;T:1477628006;N:26358	70	69	1491577735	1206599147	1229354248	1477628006	26358	ERX2443282	ERS2295356	ERA1246315	European Nucleotide Archive	Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom	2	0.91776	0.91567	0.07134	0.07241	0.7517	0.75716	0.47952	0.48745	73	73	B	B	biological fallback assumption	illumina	nextseq	full_length	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2018-03-14	Undetermined	Embryo	Blood	Hematopoietic System
8097	8097	ERR2402427	ERX2443281	ERS2295355	ERP107516	PRJEB25583	The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151	Other	The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 03 14		Hom uninj rep1	Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	SAMEA104693972	DPSQ	ENA FIRST PUBLIC:2018 10 12T17:03:15Z\|ENA LAST UPDATE:2018 03 14T19:09:14Z\|External Id:SAMEA104693972\|INSDC center name:DPSQ\|INSDC first public:2018 10 12T17:03:15Z\|INSDC last update:2018 03 14T19:09:14Z\|INSDC status:public\|Submitter Id:CM7\|common name:zebrafish\|sample name:CM7\|scientific name:Danio rerio									NextSeq 500 paired end sequencing	ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 7	unspecified	1		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	NextSeq 500	ERP107516	NextSeq 500 paired end sequencing	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 11 16	CM7.trimmed.read_1.fastq.gz CM7.trimmed.read_2.fastq.gz	fastq fastq	6262947202.0	44863127.0	ena RUN DPSQ 14 03 2018 19:09:09:420 7	0:70.28 1:69.32	A:1732018658;C:1394742098;G:1420957611;T:1715198292;N:30543	70	69	1732018658	1394742098	1420957611	1715198292	30543	ERX2443281	ERS2295355	ERA1246315	European Nucleotide Archive	Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom	2	0.91622	0.9144	0.0754	0.07588	0.74886	0.75371	0.48672	0.48471	76	76	B	B	biological fallback assumption	illumina	nextseq	full_length	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2018-03-14	Undetermined	Embryo	Blood	Hematopoietic System
8098	8098	ERR2402426	ERX2443280	ERS2295354	ERP107516	PRJEB25583	The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151	Other	The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 03 14		Het MO rep3	Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	SAMEA104693971	DPSQ	ENA FIRST PUBLIC:2018 10 12T17:03:15Z\|ENA LAST UPDATE:2018 03 14T19:09:14Z\|External Id:SAMEA104693971\|INSDC center name:DPSQ\|INSDC first public:2018 10 12T17:03:15Z\|INSDC last update:2018 03 14T19:09:14Z\|INSDC status:public\|Submitter Id:CM6\|common name:zebrafish\|sample name:CM6\|scientific name:Danio rerio									NextSeq 500 paired end sequencing	ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 6	unspecified	1		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	NextSeq 500	ERP107516	NextSeq 500 paired end sequencing	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 11 16	CM6.trimmed.read_1.fastq.gz CM6.trimmed.read_2.fastq.gz	fastq fastq	5819615834.0	41591499.0	ena RUN DPSQ 14 03 2018 19:09:09:420 6	0:70.47 1:69.45	A:1594833553;C:1309877713;G:1335153588;T:1579722744;N:28236	70	69	1594833553	1309877713	1335153588	1579722744	28236	ERX2443280	ERS2295354	ERA1246315	European Nucleotide Archive	Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom	2	0.92	0.9183	0.0573	0.05793	0.77362	0.778	0.47792	0.46987	76	75	B	B	biological fallback assumption	illumina	nextseq	full_length	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2018-03-14	Undetermined	Embryo	Blood	Hematopoietic System
8099	8099	ERR2402425	ERX2443279	ERS2295353	ERP107516	PRJEB25583	The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151	Other	The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 03 14		Het MO rep2	Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	SAMEA104693970	DPSQ	ENA FIRST PUBLIC:2018 10 12T17:03:15Z\|ENA LAST UPDATE:2018 03 14T19:09:14Z\|External Id:SAMEA104693970\|INSDC center name:DPSQ\|INSDC first public:2018 10 12T17:03:15Z\|INSDC last update:2018 03 14T19:09:14Z\|INSDC status:public\|Submitter Id:CM5\|common name:zebrafish\|sample name:CM5\|scientific name:Danio rerio									NextSeq 500 paired end sequencing	ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 5	unspecified	1		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	NextSeq 500	ERP107516	NextSeq 500 paired end sequencing	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 11 16	CM5.trimmed.read_1.fastq.gz CM5.trimmed.read_2.fastq.gz	fastq fastq	5573895202.0	39518227.0	ena RUN DPSQ 14 03 2018 19:09:09:420 5	0:71.02 1:70.03	A:1530297250;C:1251775796;G:1276506882;T:1515288256;N:27018	71	70	1530297250	1251775796	1276506882	1515288256	27018	ERX2443279	ERS2295353	ERA1246315	European Nucleotide Archive	Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom	2	0.92217	0.92081	0.06807	0.06843	0.76926	0.77441	0.45543	0.48098	76	75	B	B	biological fallback assumption	illumina	nextseq	full_length	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2018-03-14	Undetermined	Embryo	Blood	Hematopoietic System
8100	8100	ERR2402424	ERX2443278	ERS2295352	ERP107516	PRJEB25583	The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151	Other	The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 03 14		Het MO rep1	Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	SAMEA104693969	DPSQ	ENA FIRST PUBLIC:2018 10 12T17:03:15Z\|ENA LAST UPDATE:2018 03 14T19:09:14Z\|External Id:SAMEA104693969\|INSDC center name:DPSQ\|INSDC first public:2018 10 12T17:03:15Z\|INSDC last update:2018 03 14T19:09:14Z\|INSDC status:public\|Submitter Id:CM4\|common name:zebrafish\|sample name:CM4\|scientific name:Danio rerio									NextSeq 500 paired end sequencing	ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 4	unspecified	1		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	NextSeq 500	ERP107516	NextSeq 500 paired end sequencing	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 11 16	CM4.trimmed.read_1.fastq.gz CM4.trimmed.read_2.fastq.gz	fastq fastq	5803404091.0	41335851.0	ena RUN DPSQ 14 03 2018 19:09:09:420 4	0:70.72 1:69.67	A:1590577583;C:1305683925;G:1331895549;T:1575219146;N:27888	70	69	1590577583	1305683925	1331895549	1575219146	27888	ERX2443278	ERS2295352	ERA1246315	European Nucleotide Archive	Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom	2	0.9216	0.91971	0.05719	0.05738	0.77333	0.77761	0.47789	0.47244	76	74	B	B	biological fallback assumption	illumina	nextseq	full_length	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2018-03-14	Undetermined	Embryo	Blood	Hematopoietic System
8101	8101	ERR2402423	ERX2443277	ERS2295351	ERP107516	PRJEB25583	The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151	Other	The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 03 14		Het uninj rep3	Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	SAMEA104693968	DPSQ	ENA FIRST PUBLIC:2018 10 12T17:03:15Z\|ENA LAST UPDATE:2018 03 14T19:09:14Z\|External Id:SAMEA104693968\|INSDC center name:DPSQ\|INSDC first public:2018 10 12T17:03:15Z\|INSDC last update:2018 03 14T19:09:14Z\|INSDC status:public\|Submitter Id:CM3\|common name:zebrafish\|sample name:CM3\|scientific name:Danio rerio									NextSeq 500 paired end sequencing	ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 3	unspecified	1		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	NextSeq 500	ERP107516	NextSeq 500 paired end sequencing	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 11 16	CM3.trimmed.read_1.fastq.gz CM3.trimmed.read_2.fastq.gz	fastq fastq	5992797058.0	42390223.0	ena RUN DPSQ 14 03 2018 19:09:09:420 3	0:71.26 1:70.11	A:1639390320;C:1352082344;G:1378624207;T:1622672043;N:28144	71	70	1639390320	1352082344	1378624207	1622672043	28144	ERX2443277	ERS2295351	ERA1246315	European Nucleotide Archive	Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom	2	0.92104	0.92006	0.07044	0.07056	0.77506	0.78137	0.48154	0.46497	75	75	B	B	biological fallback assumption	illumina	nextseq	full_length	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2018-03-14	Undetermined	Embryo	Blood	Hematopoietic System
8102	8102	ERR2402422	ERX2443276	ERS2295350	ERP107516	PRJEB25583	The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151	Other	The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 03 14		Het uninj rep2	Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	SAMEA104693967	DPSQ	ENA FIRST PUBLIC:2018 10 12T17:03:15Z\|ENA LAST UPDATE:2018 03 14T19:09:14Z\|External Id:SAMEA104693967\|INSDC center name:DPSQ\|INSDC first public:2018 10 12T17:03:15Z\|INSDC last update:2018 03 14T19:09:14Z\|INSDC status:public\|Submitter Id:CM2\|common name:zebrafish\|sample name:CM2\|scientific name:Danio rerio									NextSeq 500 paired end sequencing	ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 2	unspecified	1		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	NextSeq 500	ERP107516	NextSeq 500 paired end sequencing	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 11 16	CM2.trimmed.read_2.fastq.gz CM2.trimmed.read_1.fastq.gz	fastq fastq	5611396868.0	39759688.0	ena RUN DPSQ 14 03 2018 19:09:09:420 2	0:71.11 1:70.02	A:1537234166;C:1262883447;G:1288444384;T:1522807333;N:27538	71	70	1537234166	1262883447	1288444384	1522807333	27538	ERX2443276	ERS2295350	ERA1246315	European Nucleotide Archive	Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom	2	0.91881	0.91733	0.06861	0.06958	0.77238	0.77883	0.48415	0.47367	76	73	B	B	biological fallback assumption	illumina	nextseq	full_length	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2018-03-14	Undetermined	Embryo	Blood	Hematopoietic System
8103	8103	ERR2402421	ERX2443275	ERS2295349	ERP107516	PRJEB25583	The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151	Other	The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform.	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 03 14		Het uninj rep1	Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos	SAMEA104693966	DPSQ	ENA FIRST PUBLIC:2018 10 12T17:03:15Z\|ENA LAST UPDATE:2018 03 14T19:09:14Z\|External Id:SAMEA104693966\|INSDC center name:DPSQ\|INSDC first public:2018 10 12T17:03:15Z\|INSDC last update:2018 03 14T19:09:14Z\|INSDC status:public\|Submitter Id:CM1\|common name:zebrafish\|sample name:CM1\|scientific name:Danio rerio									NextSeq 500 paired end sequencing	ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 1	unspecified	1		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	NextSeq 500	ERP107516	NextSeq 500 paired end sequencing	ENA FIRST PUBLIC:2018 10 12\|ENA LAST UPDATE:2018 11 16	CM1.trimmed.read_1.fastq.gz CM1.trimmed.read_2.fastq.gz	fastq fastq	6229432533.0	44233290.0	ena RUN DPSQ 14 03 2018 19:09:09:420 1	0:70.98 1:69.85	A:1712806281;C:1395764700;G:1423415860;T:1697416127;N:29565	70	69	1712806281	1395764700	1423415860	1697416127	29565	ERX2443275	ERS2295349	ERA1246315	European Nucleotide Archive	Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom	2	0.91818	0.9169	0.07104	0.07095	0.77585	0.78066	0.47896	0.46653	56	56	B	B	biological fallback assumption	illumina	nextseq	full_length	poly_a	unknown	bulk	unknown	unknown	United Kingdom	2018-03-14	Undetermined	Embryo	Blood	Hematopoietic System
24784	24784	SRR25502048	SRX21232930	SRS18488024	SRP453114	PRJNA1001808	The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger	GSE239949	Transcriptome Analysis	From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.		pubmed:28382966		Sample 15 05316 MCK mut3	GSM7678168		tissue:lyz+ mpx+ granulocytes\|cell type:lyz+ mpx+ granulocytes\|genotype:zbtb11 mutant mne\|age:48 hpf\|geo loc name:missing\|collection date:missing	Sample 15 05316 MCK mut3	Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample	lyz+ mpx+ granulocytes		RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.		cell type:lyz+ mpx+ granulocytes\|genotype:zbtb11 mutant mne\|age:48 hpf	GSM7678168	GSM7678168: Sample 15 05316 MCK mut3; Danio rerio; RNA Seq	GSM7678168 r1	GSM7678168	1	RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP453114			15-05316_MCK_mut3_GTGCTT_L002_R1_001.fastq.gz 15-05316_MCK_mut3_GTGCTT_L002_R2_001.fastq.gz	fastq fastq	4329868620.0	20618422.0	GSM7678168 r1	0:105 1:105	A:1075032412;C:1077085067;G:1119735718;T:1057797736;N:217687	105	105	1075032412	1077085067	1119735718	1057797736	217687	SRX21232930	SRS18488024	SRA1685493	Rural Clinical Sciences, La Trobe University	Rural Clinical Sciences, La Trobe University	2	0.78961	0.91048	0.20166	0.23232	0.81556	0.81115	0.59478	0.59379	105	105	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-08-03	Hatching	Embryo	Blood	Hematopoietic System
24785	24785	SRR25502049	SRX21232929	SRS18488023	SRP453114	PRJNA1001808	The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger	GSE239949	Transcriptome Analysis	From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.		pubmed:28382966		Sample 15 05316 MCK mut2	GSM7678167		tissue:lyz+ mpx+ granulocytes\|cell type:lyz+ mpx+ granulocytes\|genotype:zbtb11 mutant mne\|age:48 hpf\|geo loc name:missing\|collection date:missing	Sample 15 05316 MCK mut2	Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample	lyz+ mpx+ granulocytes		RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.		cell type:lyz+ mpx+ granulocytes\|genotype:zbtb11 mutant mne\|age:48 hpf	GSM7678167	GSM7678167: Sample 15 05316 MCK mut2; Danio rerio; RNA Seq	GSM7678167 r1	GSM7678167	1	RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP453114			15-05316_MCK_mut2_ACCTCA_L002_R1_001.fastq.gz 15-05316_MCK_mut2_ACCTCA_L002_R2_001.fastq.gz	fastq fastq	4444374270.0	21163687.0	GSM7678167 r1	0:105 1:105	A:1114919906;C:1098541058;G:1145427151;T:1085262902;N:223253	105	105	1114919906	1098541058	1145427151	1085262902	223253	SRX21232929	SRS18488023	SRA1685493	Rural Clinical Sciences, La Trobe University	Rural Clinical Sciences, La Trobe University	2	0.74961	0.90068	0.18596	0.22057	0.81115	0.80754	0.5829	0.58615	105	105	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-08-03	Hatching	Embryo	Blood	Hematopoietic System
24786	24786	SRR25502050	SRX21232928	SRS18488022	SRP453114	PRJNA1001808	The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger	GSE239949	Transcriptome Analysis	From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.		pubmed:28382966		Sample 15 05316 MCK mut1	GSM7678166		tissue:lyz+ mpx+ granulocytes\|cell type:lyz+ mpx+ granulocytes\|genotype:zbtb11 mutant mne\|age:48 hpf\|geo loc name:missing\|collection date:missing	Sample 15 05316 MCK mut1	Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample	lyz+ mpx+ granulocytes		RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.		cell type:lyz+ mpx+ granulocytes\|genotype:zbtb11 mutant mne\|age:48 hpf	GSM7678166	GSM7678166: Sample 15 05316 MCK mut1; Danio rerio; RNA Seq	GSM7678166 r1	GSM7678166	1	RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP453114			15-05316_MCK_mut1_GCACTA_L002_R1_001.fastq.gz 15-05316_MCK_mut1_GCACTA_L002_R2_001.fastq.gz	fastq fastq	4459467180.0	21235558.0	GSM7678166 r1	0:105 1:105	A:1206908747;C:1012207561;G:1060393698;T:1179731376;N:225798	105	105	1206908747	1012207561	1060393698	1179731376	225798	SRX21232928	SRS18488022	SRA1685493	Rural Clinical Sciences, La Trobe University	Rural Clinical Sciences, La Trobe University	2	0.75719	0.88462	0.20719	0.24095	0.78559	0.77914	0.50538	0.55691	105	105	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-08-03	Hatching	Embryo	Blood	Hematopoietic System
24787	24787	SRR25502051	SRX21232927	SRS18488021	SRP453114	PRJNA1001808	The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger	GSE239949	Transcriptome Analysis	From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.		pubmed:28382966		Sample 15 05315 MCK WT3	GSM7678165		tissue:lyz+ mpx+ granulocytes\|cell type:lyz+ mpx+ granulocytes\|genotype:wild type\|age:48 hpf\|geo loc name:missing\|collection date:missing	Sample 15 05315 MCK WT3	Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample	lyz+ mpx+ granulocytes		RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.		cell type:lyz+ mpx+ granulocytes\|genotype:wild type\|age:48 hpf	GSM7678165	GSM7678165: Sample 15 05315 MCK WT3; Danio rerio; RNA Seq	GSM7678165 r1	GSM7678165	1	RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP453114			15-05315_MCK_WT3_AGTGAG_L002_R1_001.fastq.gz 15-05315_MCK_WT3_AGTGAG_L002_R2_001.fastq.gz	fastq fastq	3925329240.0	18692044.0	GSM7678165 r1	0:105 1:105	A:1022654212;C:930239389;G:973328942;T:998905803;N:200894	105	105	1022654212	930239389	973328942	998905803	200894	SRX21232927	SRS18488021	SRA1685493	Rural Clinical Sciences, La Trobe University	Rural Clinical Sciences, La Trobe University	2	0.75647	0.89377	0.19165	0.22718	0.81057	0.80501	0.51173	0.54819	105	105	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-08-03	Hatching	Embryo	Blood	Hematopoietic System
24788	24788	SRR25502052	SRX21232926	SRS18488020	SRP453114	PRJNA1001808	The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger	GSE239949	Transcriptome Analysis	From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.		pubmed:28382966		Sample 15 05314 MCK WT2	GSM7678164		tissue:lyz+ mpx+ granulocytes\|cell type:lyz+ mpx+ granulocytes\|genotype:wild type\|age:48 hpf\|geo loc name:missing\|collection date:missing	Sample 15 05314 MCK WT2	Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample	lyz+ mpx+ granulocytes		RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.		cell type:lyz+ mpx+ granulocytes\|genotype:wild type\|age:48 hpf	GSM7678164	GSM7678164: Sample 15 05314 MCK WT2; Danio rerio; RNA Seq	GSM7678164 r1	GSM7678164	1	RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP453114			15-05314_MCK_WT2_TGGTGA_L002_R2_001.fastq.gz 15-05314_MCK_WT2_TGGTGA_L002_R1_001.fastq.gz	fastq fastq	4100489820.0	19526142.0	GSM7678164 r1	0:105 1:105	A:1022482319;C:1016090490;G:1063619365;T:998086417;N:211229	105	105	1022482319	1016090490	1063619365	998086417	211229	SRX21232926	SRS18488020	SRA1685493	Rural Clinical Sciences, La Trobe University	Rural Clinical Sciences, La Trobe University	2	0.76378	0.90522	0.20093	0.23619	0.82467	0.82049	0.57261	0.562	105	105	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-08-03	Hatching	Embryo	Blood	Hematopoietic System
24789	24789	SRR25502053	SRX21232925	SRS18488019	SRP453114	PRJNA1001808	The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger	GSE239949	Transcriptome Analysis	From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.		pubmed:28382966		Sample 15 05313 MCK WT1	GSM7678163		tissue:lyz+ mpx+ granulocytes\|cell type:lyz+ mpx+ granulocytes\|genotype:wild type\|age:48 hpf\|geo loc name:missing\|collection date:missing	Sample 15 05313 MCK WT1	Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample	lyz+ mpx+ granulocytes		RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.		cell type:lyz+ mpx+ granulocytes\|genotype:wild type\|age:48 hpf	GSM7678163	GSM7678163: Sample 15 05313 MCK WT1; Danio rerio; RNA Seq	GSM7678163 r1	GSM7678163	1	RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP453114			15-05313_MCK_WT1_AACCAG_L002_R1_001.fastq.gz 15-05313_MCK_WT1_AACCAG_L002_R2_001.fastq.gz	fastq fastq	4135721100.0	19693910.0	GSM7678163 r1	0:105 1:105	A:1048700719;C:1014162128;G:1070155053;T:1002495763;N:207437	105	105	1048700719	1014162128	1070155053	1002495763	207437	SRX21232925	SRS18488019	SRA1685493	Rural Clinical Sciences, La Trobe University	Rural Clinical Sciences, La Trobe University	2	0.70974	0.9073	0.1771	0.22534	0.82483	0.81625	0.56311	0.55183	105	105	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-08-03	Hatching	Embryo	Blood	Hematopoietic System
25304	25304	SRR25793376	SRX21515638	SRS18742880	SRP457465	PRJNA1010662	The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.	PRJNA1010662	Other	Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.				RNA seq Erythrocytes miR 144 adult	miR 144 adult		isolate:miR 144 mutant\|age:Adult\|collection date:N/A\|geo loc name:N/A\|sex:mixed\|tissue:Blood\|BioSampleModel:Model organism or animal									Quant seq Erythrocytes miR 144 mutant Danio rerio ADULT replicate 1	144 1 adult blood	144 1 adult blood	Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457465			DC-144AL1_S10.fastq	fastq	781435052.0	17368946.0	DC 144AL1 S10.fastq	0:44.99	A:207445570;C:148430622;G:177122903;T:245179579;N:3256378	44		207445570	148430622	177122903	245179579	3256378	SRX21515638	SRS18742880	SRA1701831	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.8759		0.28126		0.95051		0.47905		22		B		usable mapping rate	illumina	novaseq_era	3prime	poly_a	lexogen	bulk	unknown	unknown	United Kingdom	2023-08-30	Adult	Adult	Blood	Hematopoietic System
25305	25305	SRR25793377	SRX21515637	SRS18742882	SRP457465	PRJNA1010662	The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.	PRJNA1010662	Other	Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.				RNA seq Erythrocytes Wild type adult	WT adult		isolate:Wildtype\|age:Adult\|collection date:N/A\|geo loc name:N/A\|sex:mixed\|tissue:Blood\|BioSampleModel:Model organism or animal									Quant seq Erythrocytes Wild type Danio rerio ADULT replicate 3	WT3 adult blood	WT3 adult blood	Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457465			DC-WTA3_S6.fastq	fastq	601997398.0	17290043.0	DC WTA3 S6.fastq	0:34.82	A:136034449;C:142779447;G:177204517;T:134955264;N:11023721	34		136034449	142779447	177204517	134955264	11023721	SRX21515637	SRS18742882	SRA1701831	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.32909		0.08525		0.95288		0.60214		22		B		usable mapping rate	illumina	novaseq_era	3prime	poly_a	lexogen	bulk	unknown	unknown	United Kingdom	2023-08-30	Adult	Adult	Blood	Hematopoietic System
25306	25306	SRR25793378	SRX21515636	SRS18742882	SRP457465	PRJNA1010662	The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.	PRJNA1010662	Other	Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.				RNA seq Erythrocytes Wild type adult	WT adult		isolate:Wildtype\|age:Adult\|collection date:N/A\|geo loc name:N/A\|sex:mixed\|tissue:Blood\|BioSampleModel:Model organism or animal									Quant seq Erythrocytes Wild type Danio rerio ADULT replicate 2	WT2 adult blood	WT2 adult blood	Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457465			DC-WTA2_S5.fastq	fastq	669871903.0	17381581.0	DC WTA2 S5.fastq	0:38.54	A:169704437;C:140964096;G:160484620;T:189596855;N:9121895	38		169704437	140964096	160484620	189596855	9121895	SRX21515636	SRS18742882	SRA1701831	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.69865		0.19099		0.93432		0.47502		68		B		usable mapping rate	illumina	novaseq_era	3prime	poly_a	lexogen	bulk	unknown	unknown	United Kingdom	2023-08-30	Adult	Adult	Blood	Hematopoietic System
25307	25307	SRR25793379	SRX21515635	SRS18742882	SRP457465	PRJNA1010662	The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.	PRJNA1010662	Other	Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.				RNA seq Erythrocytes Wild type adult	WT adult		isolate:Wildtype\|age:Adult\|collection date:N/A\|geo loc name:N/A\|sex:mixed\|tissue:Blood\|BioSampleModel:Model organism or animal									Quant seq Erythrocytes Wild type Danio rerio ADULT replicate 1	WT1 adult blood	WT1 adult blood	Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457465			DC-WTA1_S4.fastq	fastq	824193699.0	17465379.0	DC WTA1 S4.fastq	0:47.19	A:209553199;C:169966117;G:194322860;T:244145525;N:6205998	47		209553199	169966117	194322860	244145525	6205998	SRX21515635	SRS18742882	SRA1701831	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.76241		0.25975		0.94619		0.50211		66		B		usable mapping rate	illumina	novaseq_era	3prime	poly_a	lexogen	bulk	unknown	unknown	United Kingdom	2023-08-30	Adult	Adult	Blood	Hematopoietic System
25308	25308	SRR25793380	SRX21515634	SRS18742881	SRP457465	PRJNA1010662	The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.	PRJNA1010662	Other	Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.				RNA seq Erythrocytes miR 144 embryo	miR 144 embryo		isolate:miR 144 mutant\|age:Embryo\|collection date:N/A\|geo loc name:N/A\|sex:mixed\|tissue:Blood\|BioSampleModel:Model organism or animal									Quant seq Erythrocytes miR 144 mutant Danio rerio 2 dpf replicate 3	144 3 embryo blood	144 3 embryo blood	Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457465			DC-144EL3_S18.fastq	fastq	687309797.0	17039739.0	DC 144EL3 S18.fastq	0:40.34	A:159186558;C:130452893;G:155820002;T:181676510;N:60173834	40		159186558	130452893	155820002	181676510	60173834	SRX21515634	SRS18742881	SRA1701831	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.52966		0.16941		0.97615		0.58418		61		B		usable mapping rate	illumina	novaseq_era	3prime	poly_a	lexogen	bulk	unknown	unknown	United Kingdom	2023-08-30	Hatching	Embryo	Blood	Hematopoietic System
25309	25309	SRR25793381	SRX21515633	SRS18742881	SRP457465	PRJNA1010662	The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.	PRJNA1010662	Other	Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.				RNA seq Erythrocytes miR 144 embryo	miR 144 embryo		isolate:miR 144 mutant\|age:Embryo\|collection date:N/A\|geo loc name:N/A\|sex:mixed\|tissue:Blood\|BioSampleModel:Model organism or animal									Quant seq Erythrocytes miR 144 mutant Danio rerio 2 dpf replicate 2	144 2 embryo blood	144 2 embryo blood	Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457465			DC-144EL2_S17.fastq	fastq	495318731.0	14459195.0	DC 144EL2 S17.fastq	0:34.26	A:110392869;C:106378418;G:128881687;T:107956679;N:41709078	34		110392869	106378418	128881687	107956679	41709078	SRX21515633	SRS18742881	SRA1701831	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.32147		0.04496		0.97569		0.58512		31		B		usable mapping rate	illumina	novaseq_era	3prime	poly_a	lexogen	bulk	unknown	unknown	United Kingdom	2023-08-30	Hatching	Embryo	Blood	Hematopoietic System
25310	25310	SRR25793382	SRX21515632	SRS18742881	SRP457465	PRJNA1010662	The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.	PRJNA1010662	Other	Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.				RNA seq Erythrocytes miR 144 embryo	miR 144 embryo		isolate:miR 144 mutant\|age:Embryo\|collection date:N/A\|geo loc name:N/A\|sex:mixed\|tissue:Blood\|BioSampleModel:Model organism or animal									Quant seq Erythrocytes miR 144 mutant Danio rerio 2 dpf replicate 1	144 1 embryo blood	144 1 embryo blood	Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457465			DC-144EL1_S16.fastq	fastq	974854100.0	20079553.0	DC 144EL1 S16.fastq	0:48.55	A:233861010;C:192987350;G:215192262;T:269960344;N:62853134	48		233861010	192987350	215192262	269960344	62853134	SRX21515632	SRS18742881	SRA1701831	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.77953		0.18084		0.90905		0.74157		75		B		usable mapping rate	illumina	novaseq_era	3prime	poly_a	lexogen	bulk	unknown	unknown	United Kingdom	2023-08-30	Hatching	Embryo	Blood	Hematopoietic System
25311	25311	SRR25793383	SRX21515631	SRS18742879	SRP457465	PRJNA1010662	The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.	PRJNA1010662	Other	Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.				RNA seq Erythrocytes Wild type embryo	WT embryo		isolate:Wildtype\|age:Embryo\|collection date:N/A\|geo loc name:N/A\|sex:mixed\|tissue:Blood\|BioSampleModel:Model organism or animal									Quant seq Erythrocytes Wild type Danio rerio 2 dpf replicate 3	WT3 embryo blood	WT3 embryo blood	Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457465			DC-WTE3_S15.fastq	fastq	657139116.0	15618072.0	DC WTE3 S15.fastq	0:42.08	A:154495614;C:122942896;G:147719345;T:179403193;N:52578068	42		154495614	122942896	147719345	179403193	52578068	SRX21515631	SRS18742879	SRA1701831	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.56358		0.19381		0.96757		0.6115		76		B		usable mapping rate	illumina	novaseq_era	3prime	poly_a	lexogen	bulk	unknown	unknown	United Kingdom	2023-08-30	Hatching	Embryo	Blood	Hematopoietic System
25312	25312	SRR25793384	SRX21515630	SRS18742880	SRP457465	PRJNA1010662	The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.	PRJNA1010662	Other	Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.				RNA seq Erythrocytes miR 144 adult	miR 144 adult		isolate:miR 144 mutant\|age:Adult\|collection date:N/A\|geo loc name:N/A\|sex:mixed\|tissue:Blood\|BioSampleModel:Model organism or animal									Quant seq Erythrocytes miR 144 mutant Danio rerio ADULT replicate 3	144 3 adult blood	144 3 adult blood	Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457465			DC-144AL3_S12.fastq	fastq	498938612.0	14861511.0	DC 144AL3 S12.fastq	0:33.57	A:137243823;C:96735877;G:109220779;T:152042235;N:3695898	33		137243823	96735877	109220779	152042235	3695898	SRX21515630	SRS18742880	SRA1701831	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.82213		0.16617		0.95053		0.46386		22		B		usable mapping rate	illumina	novaseq_era	3prime	poly_a	lexogen	bulk	unknown	unknown	United Kingdom	2023-08-30	Adult	Adult	Blood	Hematopoietic System
25313	25313	SRR25793385	SRX21515629	SRS18742880	SRP457465	PRJNA1010662	The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.	PRJNA1010662	Other	Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.				RNA seq Erythrocytes miR 144 adult	miR 144 adult		isolate:miR 144 mutant\|age:Adult\|collection date:N/A\|geo loc name:N/A\|sex:mixed\|tissue:Blood\|BioSampleModel:Model organism or animal									Quant seq Erythrocytes miR 144 mutant Danio rerio ADULT replicate 2	144 2 adult blood	144 2 adult blood	Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457465			DC-144AL2_S11.fastq	fastq	497890134.0	10636306.0	DC 144AL2 S11.fastq	0:46.81	A:134598214;C:94036725;G:109501897;T:158719603;N:1033695	46		134598214	94036725	109501897	158719603	1033695	SRX21515629	SRS18742880	SRA1701831	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.88496		0.29132		0.96002		0.53343		22		B		usable mapping rate	illumina	novaseq_era	3prime	poly_a	lexogen	bulk	unknown	unknown	United Kingdom	2023-08-30	Adult	Adult	Blood	Hematopoietic System
25314	25314	SRR25793386	SRX21515628	SRS18742879	SRP457465	PRJNA1010662	The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.	PRJNA1010662	Other	Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.				RNA seq Erythrocytes Wild type embryo	WT embryo		isolate:Wildtype\|age:Embryo\|collection date:N/A\|geo loc name:N/A\|sex:mixed\|tissue:Blood\|BioSampleModel:Model organism or animal									Quant seq Erythrocytes Wild type Danio rerio 2 dpf replicate 2	WT2 embryo blood	WT2 embryo blood	Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457465			DC-WTE2_S14.fastq	fastq	250958009.0	9755304.0	DC WTE2 S14.fastq	0:25.73	A:43225839;C:41823862;G:54150092;T:43159724;N:68598492	25		43225839	41823862	54150092	43159724	68598492	SRX21515628	SRS18742879	SRA1701831	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.34114		0.05466		0.96664		0.54625		47		B		usable mapping rate	illumina	novaseq_era	3prime	poly_a	lexogen	bulk	unknown	unknown	United Kingdom	2023-08-30	Hatching	Embryo	Blood	Hematopoietic System
25315	25315	SRR25793387	SRX21515627	SRS18742879	SRP457465	PRJNA1010662	The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.	PRJNA1010662	Other	Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.				RNA seq Erythrocytes Wild type embryo	WT embryo		isolate:Wildtype\|age:Embryo\|collection date:N/A\|geo loc name:N/A\|sex:mixed\|tissue:Blood\|BioSampleModel:Model organism or animal									Quant seq Erythrocytes Wild type Danio rerio 2 dpf replicate 1	WT1 embryo blood	WT1 embryo blood	Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP457465			DC-WTE1_S13.fastq	fastq	816518564.0	19556325.0	DC WTE1 S13.fastq	0:41.75	A:187091550;C:151287428;G:179967901;T:221475884;N:76695801	41		187091550	151287428	179967901	221475884	76695801	SRX21515627	SRS18742879	SRA1701831	University of East Anglia\|Biological Sciences	University of East Anglia	1	0.61681		0.1874		0.95101		0.56879		29		B		usable mapping rate	illumina	novaseq_era	3prime	poly_a	lexogen	bulk	unknown	unknown	United Kingdom	2023-08-30	Hatching	Embryo	Blood	Hematopoietic System
28389	28389	SRR26213385	SRX21923919	SRS19008430	SRP463773	PRJNA1022165	Transcriptomic analysis of Per2 deficient neutrophils compared WT neutrophils following infection.	GSE244308	Transcriptome Analysis	Functional analysis demonstrates that neutrophils deficient in Per2 have reduced bactericidal activity when compared WT neutrophils. Overall design: Differential gene expression analysis of RNA seq data from Per2 deficient neutrophils and WT neutrophils post Salmonella typhimurium infection in biological quadruplet.				Neutrophils WT infected 4	GSM7813285		tissue:Neutrophil\|developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2/WT\|infection:Salm1lla typhimurium\|geo loc name:missing\|collection date:missing	Neutrophils WT infected 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyze the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz10 Supplementary files format and content: Comma separated values file show FPKM Log2FC and adj P value of DEGs comparing Per2Infected and WTInfected samples.	Neutrophil	At 52 hpf 4 hours post lights on Tglyz:DsRED2/WT and Tglyz:DsRED2;per2 / zebrafish larvae we infected with 1 000 CFU Salmonella Typhimurium and neutrophils were isolated at 3 hours post infection by FACS.	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C under standard light:dark conditions	developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2/WT\|infection:Salm1lla typhimurium	GSM7813285	GSM7813285: Neutrophils WT infected 4; Danio rerio; RNA Seq	GSM7813285 r1	GSM7813285	1	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP463773		loader:fastq load.py	WTInfected-4_S8_R1_001.fastq.gz	fastq	2240130033.0	29683768.0	GSM7813285 r1	0:75.47	A:639465198;C:479506246;G:493408026;T:627654835;N:95728	75		639465198	479506246	493408026	627654835	95728	SRX21923919	SRS19008430	SRA1722831	The University of Auckland	The University of Auckland	1	0.89082		0.28084		0.75523		0.4978		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2023-09-28	Larval	Larval	Blood	Hematopoietic System
28390	28390	SRR26213386	SRX21923918	SRS19008429	SRP463773	PRJNA1022165	Transcriptomic analysis of Per2 deficient neutrophils compared WT neutrophils following infection.	GSE244308	Transcriptome Analysis	Functional analysis demonstrates that neutrophils deficient in Per2 have reduced bactericidal activity when compared WT neutrophils. Overall design: Differential gene expression analysis of RNA seq data from Per2 deficient neutrophils and WT neutrophils post Salmonella typhimurium infection in biological quadruplet.				Neutrophils WT infected 3	GSM7813284		tissue:Neutrophil\|developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2/WT\|infection:Salm1lla typhimurium\|geo loc name:missing\|collection date:missing	Neutrophils WT infected 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyze the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz10 Supplementary files format and content: Comma separated values file show FPKM Log2FC and adj P value of DEGs comparing Per2Infected and WTInfected samples.	Neutrophil	At 52 hpf 4 hours post lights on Tglyz:DsRED2/WT and Tglyz:DsRED2;per2 / zebrafish larvae we infected with 1 000 CFU Salmonella Typhimurium and neutrophils were isolated at 3 hours post infection by FACS.	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C under standard light:dark conditions	developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2/WT\|infection:Salm1lla typhimurium	GSM7813284	GSM7813284: Neutrophils WT infected 3; Danio rerio; RNA Seq	GSM7813284 r1	GSM7813284	1	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP463773		loader:fastq load.py	WTInfected-3_S7_R1_001.fastq.gz	fastq	2789643441.0	37059064.0	GSM7813284 r1	0:75.28	A:770315857;C:626379098;G:642210747;T:750373702;N:364037	75		770315857	626379098	642210747	750373702	364037	SRX21923918	SRS19008429	SRA1722831	The University of Auckland	The University of Auckland	1	0.89494		0.12907		0.81154		0.50044		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2023-09-28	Larval	Larval	Blood	Hematopoietic System
28391	28391	SRR26213387	SRX21923917	SRS19008428	SRP463773	PRJNA1022165	Transcriptomic analysis of Per2 deficient neutrophils compared WT neutrophils following infection.	GSE244308	Transcriptome Analysis	Functional analysis demonstrates that neutrophils deficient in Per2 have reduced bactericidal activity when compared WT neutrophils. Overall design: Differential gene expression analysis of RNA seq data from Per2 deficient neutrophils and WT neutrophils post Salmonella typhimurium infection in biological quadruplet.				Neutrophils WT infected 2	GSM7813283		tissue:Neutrophil\|developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2/WT\|infection:Salm1lla typhimurium\|geo loc name:missing\|collection date:missing	Neutrophils WT infected 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyze the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz10 Supplementary files format and content: Comma separated values file show FPKM Log2FC and adj P value of DEGs comparing Per2Infected and WTInfected samples.	Neutrophil	At 52 hpf 4 hours post lights on Tglyz:DsRED2/WT and Tglyz:DsRED2;per2 / zebrafish larvae we infected with 1 000 CFU Salmonella Typhimurium and neutrophils were isolated at 3 hours post infection by FACS.	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C under standard light:dark conditions	developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2/WT\|infection:Salm1lla typhimurium	GSM7813283	GSM7813283: Neutrophils WT infected 2; Danio rerio; RNA Seq	GSM7813283 r1	GSM7813283	1	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP463773		loader:fastq load.py	WTInfected-2_S6_R1_001.fastq.gz	fastq	2502579643.0	33171064.0	GSM7813283 r1	0:75.44	A:690295075;C:562877524;G:577315919;T:671999174;N:91951	75		690295075	562877524	577315919	671999174	91951	SRX21923917	SRS19008428	SRA1722831	The University of Auckland	The University of Auckland	1	0.89596		0.11653		0.82562		0.47762		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2023-09-28	Larval	Larval	Blood	Hematopoietic System
28392	28392	SRR26213388	SRX21923916	SRS19008427	SRP463773	PRJNA1022165	Transcriptomic analysis of Per2 deficient neutrophils compared WT neutrophils following infection.	GSE244308	Transcriptome Analysis	Functional analysis demonstrates that neutrophils deficient in Per2 have reduced bactericidal activity when compared WT neutrophils. Overall design: Differential gene expression analysis of RNA seq data from Per2 deficient neutrophils and WT neutrophils post Salmonella typhimurium infection in biological quadruplet.				Neutrophils WT infected 1	GSM7813282		tissue:Neutrophil\|developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2/WT\|infection:Salm1lla typhimurium\|geo loc name:missing\|collection date:missing	Neutrophils WT infected 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyze the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz10 Supplementary files format and content: Comma separated values file show FPKM Log2FC and adj P value of DEGs comparing Per2Infected and WTInfected samples.	Neutrophil	At 52 hpf 4 hours post lights on Tglyz:DsRED2/WT and Tglyz:DsRED2;per2 / zebrafish larvae we infected with 1 000 CFU Salmonella Typhimurium and neutrophils were isolated at 3 hours post infection by FACS.	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C under standard light:dark conditions	developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2/WT\|infection:Salm1lla typhimurium	GSM7813282	GSM7813282: Neutrophils WT infected 1; Danio rerio; RNA Seq	GSM7813282 r1	GSM7813282	1	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP463773		loader:fastq load.py	WTInfected-1_S5_R1_001.fastq.gz	fastq	2629109363.0	34890907.0	GSM7813282 r1	0:75.35	A:717313087;C:596048245;G:613729475;T:701790568;N:227988	75		717313087	596048245	613729475	701790568	227988	SRX21923916	SRS19008427	SRA1722831	The University of Auckland	The University of Auckland	1	0.88964		0.13171		0.81142		0.49273		73		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2023-09-28	Larval	Larval	Blood	Hematopoietic System
28393	28393	SRR26213389	SRX21923915	SRS19008426	SRP463773	PRJNA1022165	Transcriptomic analysis of Per2 deficient neutrophils compared WT neutrophils following infection.	GSE244308	Transcriptome Analysis	Functional analysis demonstrates that neutrophils deficient in Per2 have reduced bactericidal activity when compared WT neutrophils. Overall design: Differential gene expression analysis of RNA seq data from Per2 deficient neutrophils and WT neutrophils post Salmonella typhimurium infection in biological quadruplet.				Neutrophils per2 infected 4	GSM7813281		tissue:Neutrophil\|developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2;per2 / \|infection:Salm1lla typhimurium\|geo loc name:missing\|collection date:missing	Neutrophils per2 infected 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyze the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz10 Supplementary files format and content: Comma separated values file show FPKM Log2FC and adj P value of DEGs comparing Per2Infected and WTInfected samples.	Neutrophil	At 52 hpf 4 hours post lights on Tglyz:DsRED2/WT and Tglyz:DsRED2;per2 / zebrafish larvae we infected with 1 000 CFU Salmonella Typhimurium and neutrophils were isolated at 3 hours post infection by FACS.	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C under standard light:dark conditions	developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2;per2 / \|infection:Salm1lla typhimurium	GSM7813281	GSM7813281: Neutrophils per2 infected 4; Danio rerio; RNA Seq	GSM7813281 r1	GSM7813281	1	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP463773		loader:fastq load.py	per2Infected-4_S16_R1_001.fastq.gz	fastq	2915831120.0	38708122.0	GSM7813281 r1	0:75.33	A:819771092;C:637630362;G:654348519;T:803699649;N:381498	75		819771092	637630362	654348519	803699649	381498	SRX21923915	SRS19008426	SRA1722831	The University of Auckland	The University of Auckland	1	0.90568		0.15837		0.82055		0.49547		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2023-09-28	Larval	Larval	Blood	Hematopoietic System
28394	28394	SRR26213390	SRX21923914	SRS19008425	SRP463773	PRJNA1022165	Transcriptomic analysis of Per2 deficient neutrophils compared WT neutrophils following infection.	GSE244308	Transcriptome Analysis	Functional analysis demonstrates that neutrophils deficient in Per2 have reduced bactericidal activity when compared WT neutrophils. Overall design: Differential gene expression analysis of RNA seq data from Per2 deficient neutrophils and WT neutrophils post Salmonella typhimurium infection in biological quadruplet.				Neutrophils per2 infected 3	GSM7813280		tissue:Neutrophil\|developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2;per2 / \|infection:Salm1lla typhimurium\|geo loc name:missing\|collection date:missing	Neutrophils per2 infected 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyze the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz10 Supplementary files format and content: Comma separated values file show FPKM Log2FC and adj P value of DEGs comparing Per2Infected and WTInfected samples.	Neutrophil	At 52 hpf 4 hours post lights on Tglyz:DsRED2/WT and Tglyz:DsRED2;per2 / zebrafish larvae we infected with 1 000 CFU Salmonella Typhimurium and neutrophils were isolated at 3 hours post infection by FACS.	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C under standard light:dark conditions	developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2;per2 / \|infection:Salm1lla typhimurium	GSM7813280	GSM7813280: Neutrophils per2 infected 3; Danio rerio; RNA Seq	GSM7813280 r1	GSM7813280	1	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP463773		loader:fastq load.py	per2Infected-3_S15_R1_001.fastq.gz	fastq	2622630688.0	34745018.0	GSM7813280 r1	0:75.48	A:726047024;C:584906297;G:600999032;T:710582433;N:95902	75		726047024	584906297	600999032	710582433	95902	SRX21923914	SRS19008425	SRA1722831	The University of Auckland	The University of Auckland	1	0.91129		0.1229		0.81345		0.48284		75		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2023-09-28	Larval	Larval	Blood	Hematopoietic System
28395	28395	SRR26213391	SRX21923913	SRS19008424	SRP463773	PRJNA1022165	Transcriptomic analysis of Per2 deficient neutrophils compared WT neutrophils following infection.	GSE244308	Transcriptome Analysis	Functional analysis demonstrates that neutrophils deficient in Per2 have reduced bactericidal activity when compared WT neutrophils. Overall design: Differential gene expression analysis of RNA seq data from Per2 deficient neutrophils and WT neutrophils post Salmonella typhimurium infection in biological quadruplet.				Neutrophils per2 infected 2	GSM7813279		tissue:Neutrophil\|developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2;per2 / \|infection:Salm1lla typhimurium\|geo loc name:missing\|collection date:missing	Neutrophils per2 infected 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyze the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz10 Supplementary files format and content: Comma separated values file show FPKM Log2FC and adj P value of DEGs comparing Per2Infected and WTInfected samples.	Neutrophil	At 52 hpf 4 hours post lights on Tglyz:DsRED2/WT and Tglyz:DsRED2;per2 / zebrafish larvae we infected with 1 000 CFU Salmonella Typhimurium and neutrophils were isolated at 3 hours post infection by FACS.	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C under standard light:dark conditions	developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2;per2 / \|infection:Salm1lla typhimurium	GSM7813279	GSM7813279: Neutrophils per2 infected 2; Danio rerio; RNA Seq	GSM7813279 r1	GSM7813279	1	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP463773		loader:fastq load.py	per2Infected-2_S14_R1_001.fastq.gz	fastq	2152892336.0	28547218.0	GSM7813279 r1	0:75.42	A:594950127;C:480727855;G:495163350;T:581915730;N:135274	75		594950127	480727855	495163350	581915730	135274	SRX21923913	SRS19008424	SRA1722831	The University of Auckland	The University of Auckland	1	0.9068		0.11944		0.82804		0.48956		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2023-09-28	Larval	Larval	Blood	Hematopoietic System
28396	28396	SRR26213392	SRX21923912	SRS19008423	SRP463773	PRJNA1022165	Transcriptomic analysis of Per2 deficient neutrophils compared WT neutrophils following infection.	GSE244308	Transcriptome Analysis	Functional analysis demonstrates that neutrophils deficient in Per2 have reduced bactericidal activity when compared WT neutrophils. Overall design: Differential gene expression analysis of RNA seq data from Per2 deficient neutrophils and WT neutrophils post Salmonella typhimurium infection in biological quadruplet.				Neutrophils per2 infected 1	GSM7813278		tissue:Neutrophil\|developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2;per2 / \|infection:Salm1lla typhimurium\|geo loc name:missing\|collection date:missing	Neutrophils per2 infected 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyze the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz10 Supplementary files format and content: Comma separated values file show FPKM Log2FC and adj P value of DEGs comparing Per2Infected and WTInfected samples.	Neutrophil	At 52 hpf 4 hours post lights on Tglyz:DsRED2/WT and Tglyz:DsRED2;per2 / zebrafish larvae we infected with 1 000 CFU Salmonella Typhimurium and neutrophils were isolated at 3 hours post infection by FACS.	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C under standard light:dark conditions	developmental stage:larvae\|cell type:Neutrophil\|genotype:Tglyz:DsRED2;per2 / \|infection:Salm1lla typhimurium	GSM7813278	GSM7813278: Neutrophils per2 infected 1; Danio rerio; RNA Seq	GSM7813278 r1	GSM7813278	1	Larvae were homogenized in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1 000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP463773		loader:fastq load.py	per2Infcted-1_S13_R1_001.fastq.gz	fastq	2276537599.0	30215018.0	GSM7813278 r1	0:75.34	A:614225653;C:523562022;G:541795396;T:596817124;N:137404	75		614225653	523562022	541795396	596817124	137404	SRX21923912	SRS19008423	SRA1722831	The University of Auckland	The University of Auckland	1	0.92361		0.09247		0.81324		0.46862		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	New Zealand	2023-09-28	Larval	Larval	Blood	Hematopoietic System
28902	28902	SRR26827532	SRX22524052	SRS19535497	SRP471831	PRJNA1040223	The Caudal Hematopoietic Tissue is Differentially Required for Erythrocytes and Neutrophils from Definitive Hematopoiesis in Zebrafish	GSE247730	Transcriptome Analysis	Neutrophils and erythrocytes are vital to the immune system and oxygen transport respectively. However the mechanisms by which hematopoietic niches support their development remain incompletely understood. In hematopoiesis research zebrafish larvae are a common model for studying the development of definitive neutrophils and erythrocytes in the caudal hematopoietic tissue. In this study we showed that erythrocytes predominantly reside inside the blood vessels of the CHT while neutrophils stay outside. Ectopic vascular endothelium induced by Bone Morphogenetic Protein 2bBmp2b overexpression attracts both cell types with erythrocytes inside and neutrophils outside. CHT removal has minimal impact on definitive neutrophils from the ventral wall of the dorsal aorta VDA but severely affects definitive erythrocytes from the same source. Bulk RNA sequencing identified epoa as a vital factor for erythrocyte generation within CHT endothelium. Overexpression of epoa through the lyve1b promoter which is specifically expressed in vein lymphatic vessels and CHT vein endothelial cells rescued the erythrocyte reduction in epoa mutants. Our study reveals that the caudal hematopoietic tissue is differentially required for definitive erythrocytes and neutrophils. Overall design: We then performed gene expression profiling analysis using data obtained from BULK RNA seq of 5dpf vein endothelium cells and endothelium cells.				vein endothelium cells Day5 rep2	GSM7899809		source name:Caudal hematopoietic tissue\|tissue:Caudal hematopoietic tissue\|cell type:vein endothelium cells\|genotype:Wildtype\|treatment:no treatment\|geo loc name:missing\|collection date:missing	vein endothelium cells Day5 rep2	Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value≤20 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 with “ rna strandness RF” and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments Principal component analysis PCA was performed with R package gmodels http://www.r project.org/ in this experience;RNAs differential expression analysis was performed by DESeq2; Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample	Caudal hematopoietic tissue		Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.		tissue:Caudal hematopoietic tissue\|cell type:vein endothelium cells\|genotype:Wildtype\|treatment:no treatment	GSM7899809	GSM7899809: vein endothelium cells Day5 rep2; Danio rerio; RNA Seq	GSM7899809 r1	GSM7899809	1	Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP471831		loader:fastq load.py	vein_endothelium_cells-2_1.fq.gz vein_endothelium_cells-2_2.fq.gz	fastq fastq	9110989800.0	30369966.0	GSM7899809 r1	0:150 1:150	A:2454542720;C:2090617752;G:2126374129;T:2439172440;N:282759	150	150	2454542720	2090617752	2126374129	2439172440	282759	SRX22524052	SRS19535497	SRA1750986	South China University of Technology	South China University of Technology	2	0.89413	0.89048	0.1507	0.14922	0.78466	0.78496	0.5263	0.5335	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2023-11-14	Larval	Larval	Blood	Hematopoietic System
28903	28903	SRR26827533	SRX22524051	SRS19535496	SRP471831	PRJNA1040223	The Caudal Hematopoietic Tissue is Differentially Required for Erythrocytes and Neutrophils from Definitive Hematopoiesis in Zebrafish	GSE247730	Transcriptome Analysis	Neutrophils and erythrocytes are vital to the immune system and oxygen transport respectively. However the mechanisms by which hematopoietic niches support their development remain incompletely understood. In hematopoiesis research zebrafish larvae are a common model for studying the development of definitive neutrophils and erythrocytes in the caudal hematopoietic tissue. In this study we showed that erythrocytes predominantly reside inside the blood vessels of the CHT while neutrophils stay outside. Ectopic vascular endothelium induced by Bone Morphogenetic Protein 2bBmp2b overexpression attracts both cell types with erythrocytes inside and neutrophils outside. CHT removal has minimal impact on definitive neutrophils from the ventral wall of the dorsal aorta VDA but severely affects definitive erythrocytes from the same source. Bulk RNA sequencing identified epoa as a vital factor for erythrocyte generation within CHT endothelium. Overexpression of epoa through the lyve1b promoter which is specifically expressed in vein lymphatic vessels and CHT vein endothelial cells rescued the erythrocyte reduction in epoa mutants. Our study reveals that the caudal hematopoietic tissue is differentially required for definitive erythrocytes and neutrophils. Overall design: We then performed gene expression profiling analysis using data obtained from BULK RNA seq of 5dpf vein endothelium cells and endothelium cells.				vein endothelium cells Day5 rep1	GSM7899808		source name:Caudal hematopoietic tissue\|tissue:Caudal hematopoietic tissue\|cell type:vein endothelium cells\|genotype:Wildtype\|treatment:no treatment\|geo loc name:missing\|collection date:missing	vein endothelium cells Day5 rep1	Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value≤20 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 with “ rna strandness RF” and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments Principal component analysis PCA was performed with R package gmodels http://www.r project.org/ in this experience;RNAs differential expression analysis was performed by DESeq2; Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample	Caudal hematopoietic tissue		Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.		tissue:Caudal hematopoietic tissue\|cell type:vein endothelium cells\|genotype:Wildtype\|treatment:no treatment	GSM7899808	GSM7899808: vein endothelium cells Day5 rep1; Danio rerio; RNA Seq	GSM7899808 r1	GSM7899808	1	Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP471831		loader:fastq load.py	vein_endothelium_cells-1_2.fq.gz vein_endothelium_cells-1_1.fq.gz	fastq fastq	8585973300.0	28619911.0	GSM7899808 r1	0:150 1:150	A:2253650188;C:2015841518;G:2037568162;T:2278266858;N:646574	150	150	2253650188	2015841518	2037568162	2278266858	646574	SRX22524051	SRS19535496	SRA1750986	South China University of Technology	South China University of Technology	2	0.8876	0.88392	0.14777	0.14719	0.78969	0.79038	0.53142	0.53136	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2023-11-14	Larval	Larval	Blood	Hematopoietic System
28904	28904	SRR26827534	SRX22524050	SRS19535495	SRP471831	PRJNA1040223	The Caudal Hematopoietic Tissue is Differentially Required for Erythrocytes and Neutrophils from Definitive Hematopoiesis in Zebrafish	GSE247730	Transcriptome Analysis	Neutrophils and erythrocytes are vital to the immune system and oxygen transport respectively. However the mechanisms by which hematopoietic niches support their development remain incompletely understood. In hematopoiesis research zebrafish larvae are a common model for studying the development of definitive neutrophils and erythrocytes in the caudal hematopoietic tissue. In this study we showed that erythrocytes predominantly reside inside the blood vessels of the CHT while neutrophils stay outside. Ectopic vascular endothelium induced by Bone Morphogenetic Protein 2bBmp2b overexpression attracts both cell types with erythrocytes inside and neutrophils outside. CHT removal has minimal impact on definitive neutrophils from the ventral wall of the dorsal aorta VDA but severely affects definitive erythrocytes from the same source. Bulk RNA sequencing identified epoa as a vital factor for erythrocyte generation within CHT endothelium. Overexpression of epoa through the lyve1b promoter which is specifically expressed in vein lymphatic vessels and CHT vein endothelial cells rescued the erythrocyte reduction in epoa mutants. Our study reveals that the caudal hematopoietic tissue is differentially required for definitive erythrocytes and neutrophils. Overall design: We then performed gene expression profiling analysis using data obtained from BULK RNA seq of 5dpf vein endothelium cells and endothelium cells.				non vein endothelium cells Control Day5 rep2	GSM7899807		source name:Caudal hematopoietic tissue\|tissue:Caudal hematopoietic tissue\|cell type:non vein endothelium cells\|genotype:Wildtype\|treatment:no treatment\|geo loc name:missing\|collection date:missing	non vein endothelium cells Control Day5 rep2	Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value≤20 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 with “ rna strandness RF” and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments Principal component analysis PCA was performed with R package gmodels http://www.r project.org/ in this experience;RNAs differential expression analysis was performed by DESeq2; Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample	Caudal hematopoietic tissue		Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.		tissue:Caudal hematopoietic tissue\|cell type:non vein endothelium cells\|genotype:Wildtype\|treatment:no treatment	GSM7899807	GSM7899807: non vein endothelium cells Control Day5 rep2; Danio rerio; RNA Seq	GSM7899807 r1	GSM7899807	1	Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP471831		loader:fastq load.py	non-vein_endothelium_cells-2_1.fq.gz non-vein_endothelium_cells-2_2.fq.gz	fastq fastq	9363942600.0	31213142.0	GSM7899807 r1	0:150 1:150	A:2523111369;C:2155598161;G:2171776473;T:2513164552;N:292045	150	150	2523111369	2155598161	2171776473	2513164552	292045	SRX22524050	SRS19535495	SRA1750986	South China University of Technology	South China University of Technology	2	0.93879	0.93706	0.10971	0.10945	0.76721	0.76737	0.51346	0.51513	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2023-11-14	Larval	Larval	Blood	Hematopoietic System
28905	28905	SRR26827535	SRX22524049	SRS19535494	SRP471831	PRJNA1040223	The Caudal Hematopoietic Tissue is Differentially Required for Erythrocytes and Neutrophils from Definitive Hematopoiesis in Zebrafish	GSE247730	Transcriptome Analysis	Neutrophils and erythrocytes are vital to the immune system and oxygen transport respectively. However the mechanisms by which hematopoietic niches support their development remain incompletely understood. In hematopoiesis research zebrafish larvae are a common model for studying the development of definitive neutrophils and erythrocytes in the caudal hematopoietic tissue. In this study we showed that erythrocytes predominantly reside inside the blood vessels of the CHT while neutrophils stay outside. Ectopic vascular endothelium induced by Bone Morphogenetic Protein 2bBmp2b overexpression attracts both cell types with erythrocytes inside and neutrophils outside. CHT removal has minimal impact on definitive neutrophils from the ventral wall of the dorsal aorta VDA but severely affects definitive erythrocytes from the same source. Bulk RNA sequencing identified epoa as a vital factor for erythrocyte generation within CHT endothelium. Overexpression of epoa through the lyve1b promoter which is specifically expressed in vein lymphatic vessels and CHT vein endothelial cells rescued the erythrocyte reduction in epoa mutants. Our study reveals that the caudal hematopoietic tissue is differentially required for definitive erythrocytes and neutrophils. Overall design: We then performed gene expression profiling analysis using data obtained from BULK RNA seq of 5dpf vein endothelium cells and endothelium cells.				non vein endothelium cells Control Day5 rep1	GSM7899806		source name:Caudal hematopoietic tissue\|tissue:Caudal hematopoietic tissue\|cell type:non vein endothelium cells\|genotype:Wildtype\|treatment:no treatment\|geo loc name:missing\|collection date:missing	non vein endothelium cells Control Day5 rep1	Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value≤20 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 with “ rna strandness RF” and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments Principal component analysis PCA was performed with R package gmodels http://www.r project.org/ in this experience;RNAs differential expression analysis was performed by DESeq2; Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample	Caudal hematopoietic tissue		Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.		tissue:Caudal hematopoietic tissue\|cell type:non vein endothelium cells\|genotype:Wildtype\|treatment:no treatment	GSM7899806	GSM7899806: non vein endothelium cells Control Day5 rep1; Danio rerio; RNA Seq	GSM7899806 r1	GSM7899806	1	Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP471831		loader:fastq load.py	non-vein_endothelium_cells-1_1.fq.gz non-vein_endothelium_cells-1_2.fq.gz	fastq fastq	8396176800.0	27987256.0	GSM7899806 r1	0:150 1:150	A:2190594419;C:1990596503;G:2019391921;T:2194713332;N:880625	150	150	2190594419	1990596503	2019391921	2194713332	880625	SRX22524049	SRS19535494	SRA1750986	South China University of Technology	South China University of Technology	2	0.94508	0.94385	0.0967	0.09697	0.77642	0.77632	0.49896	0.49962	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2023-11-14	Larval	Larval	Blood	Hematopoietic System
30018	30018	SRR27988043	SRX23641260	SRS20476222	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.				hamp / 36 hpf blood	zebrafish hamp / 36 hpf blood replicate 3		strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:36 hpf\|dev stage:36 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:blood\|genotype:hamp knockdown\|sample type:tissue sample\|treatment:replicate 3\|BioSampleModel:Model organism or animal									RNA seq hamp / 36 hpf blood replicate 3	B 6	B 6	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064			KO-3_R2_001.fastq.gz KO-3_R1_001.fastq.gz	fastq fastq	8752665900.0	29175553.0	KO 3 R1 001.fastq.gz	0:150 1:150	A:2204170575;C:2174083961;G:2224694970;T:2149603712;N:112682	150	150	2204170575	2174083961	2224694970	2149603712	112682	SRX23641260	SRS20476222	SRA1803422	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.91553	0.91645	0.01276	0.01288	0.85884	0.85839	0.35101	0.40996	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-02-16	Pharyngula	Embryo	Blood	Hematopoietic System
30019	30019	SRR27988044	SRX23641259	SRS20476221	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.				hamp / 36 hpf blood	zebrafish hamp / 36 hpf blood replicate 2		strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:36 hpf\|dev stage:36 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:blood\|genotype:hamp knockdown\|sample type:tissue sample\|treatment:replicate 2\|BioSampleModel:Model organism or animal									RNA seq hamp / 36 hpf blood replicate 2	B 5	B 5	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064			KO-2_R1_001.fastq.gz KO-2_R2_001.fastq.gz	fastq fastq	8060498700.0	26868329.0	KO 2 R1 001.fastq.gz	0:150 1:150	A:2045797336;C:1985847523;G:2035528018;T:1993222840;N:102983	150	150	2045797336	1985847523	2035528018	1993222840	102983	SRX23641259	SRS20476221	SRA1803422	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.9213	0.92027	0.0167	0.01676	0.8242	0.82475	0.41081	0.41111	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-02-16	Pharyngula	Embryo	Blood	Hematopoietic System
30020	30020	SRR27988045	SRX23641258	SRS20476220	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.				hamp / 36 hpf blood	zebrafish hamp / 36 hpf blood replicate 1		strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:36 hpf\|dev stage:36 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:blood\|genotype:hamp knockdown\|sample type:tissue sample\|treatment:replicate 1\|BioSampleModel:Model organism or animal									RNA seq hamp / 36 hpf blood replicate 1	B 4	B 4	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064			KO-1_R1_001.fastq.gz KO-1_R2_001.fastq.gz	fastq fastq	8707637700.0	29025459.0	KO 1 R1 001.fastq.gz	0:150 1:150	A:2222026435;C:2133480283;G:2182087972;T:2169932447;N:110563	150	150	2222026435	2133480283	2182087972	2169932447	110563	SRX23641258	SRS20476220	SRA1803422	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.91531	0.91359	0.02185	0.0221	0.81213	0.8128	0.37868	0.42351	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-02-16	Pharyngula	Embryo	Blood	Hematopoietic System
30021	30021	SRR27988046	SRX23641257	SRS20476219	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.				wild type 36 hpf blood	zebrafish wild type 36 hpf blood replicate 3		strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:36 hpf\|dev stage:36 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:blood\|genotype:wild type\|sample type:tissue sample\|treatment:replicate 3\|BioSampleModel:Model organism or animal									RNA seq wild type 36 hpf blood replicate 3	B 3	B 3	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064			WT-3_R1_001.fastq.gz WT-3_R2_001.fastq.gz	fastq fastq	8829371400.0	29431238.0	WT 3 R1 001.fastq.gz	0:150 1:150	A:2278837675;C:2141723937;G:2193442375;T:2215253519;N:113894	150	150	2278837675	2141723937	2193442375	2215253519	113894	SRX23641257	SRS20476219	SRA1803422	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.90531	0.9043	0.03015	0.03017	0.8101	0.8112	0.43085	0.43002	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-02-16	Pharyngula	Embryo	Blood	Hematopoietic System
30022	30022	SRR27988047	SRX23641256	SRS20476218	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.				wild type 36 hpf blood	zebrafish wild type 36 hpf blood replicate 2		strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:36 hpf\|dev stage:36 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:blood\|genotype:wild type\|sample type:tissue sample\|treatment:replicate 2\|BioSampleModel:Model organism or animal									RNA seq wild type 36 hpf blood replicate 2	B 2	B 2	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064			WT-2_R1_001.fastq.gz WT-2_R2_001.fastq.gz	fastq fastq	7365643800.0	24552146.0	WT 2 R1 001.fastq.gz	0:150 1:150	A:1867985067;C:1819016430;G:1870006707;T:1808540769;N:94827	150	150	1867985067	1819016430	1870006707	1808540769	94827	SRX23641256	SRS20476218	SRA1803422	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.90612	0.90536	0.01714	0.01746	0.88109	0.88156	0.32469	0.39232	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-02-16	Pharyngula	Embryo	Blood	Hematopoietic System
30023	30023	SRR27988048	SRX23641255	SRS20476217	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.				wild type 36 hpf blood	zebrafish wild type 36 hpf blood replicate 1		strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:36 hpf\|dev stage:36 hpf\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:blood\|genotype:wild type\|sample type:tissue sample\|treatment:replicate 1\|BioSampleModel:Model organism or animal									RNA seq wild type 36 hpf blood replicate 1	B 1	B 1	bulk RNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064			WT-1_R1_001.fastq.gz WT-1_R2_001.fastq.gz	fastq fastq	8631863400.0	28772878.0	WT 1 R1 001.fastq.gz	0:150 1:150	A:2186212554;C:2135990723;G:2179142081;T:2130408485;N:109557	150	150	2186212554	2135990723	2179142081	2130408485	109557	SRX23641255	SRS20476217	SRA1803422	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.90461	0.90281	0.01388	0.01365	0.83871	0.83895	0.36511	0.41074	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2024-02-16	Pharyngula	Embryo	Blood	Hematopoietic System
30066	30066	SRR27676305	SRX23343658	SRS20205511	SRP485121	PRJNA1067443	RNA seq&smart seq&CUT TAG	PRJNA1067443	Other	RNA seq&smart seq&CUT TAG					smart seq of setdb1b mt 2		strain:missing\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:missing\|dev stage:96hpf\|collection date:missing\|geo loc name:missing\|sex:pooled male and female\|tissue:hematopoietic stem and progenitor cell\|replicate:replicate = biological replicate 2\|id</u><u>:9</u><u>\|BioSampleModel:Model organism or animal									smart seq of setdb1b mt 2	smart seq of setdb1b mt 2	smart seq of setdb1b mt 2	smart seq of setdb1b mt of replicate 2		RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485121			smart-seq of setdb1b mt_2_R2.fastq.gz.gz smart-seq of setdb1b mt_2_R1.fastq.gz.gz	fastq fastq	11957458200.0	39858194.0	smart seq of setdb1b mt 2 R1.fastq.gz.gz	0:150 1:150	A:3692371435;C:1893324720;G:2810967928;T:3560751613;N:42504	150	150	3692371435	1893324720	2810967928	3560751613	42504	SRX23343658	SRS20205511	SRA1789215	East China Normal University\|Institute of Biomedical Sciences	East China Normal University	2	0.76332	0.82639	0.22191	0.23939	0.87093	0.87117	0.59757	0.60008	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-01-22	Larval	Larval	Blood	Hematopoietic System
30067	30067	SRR27676306	SRX23343657	SRS20205510	SRP485121	PRJNA1067443	RNA seq&smart seq&CUT TAG	PRJNA1067443	Other	RNA seq&smart seq&CUT TAG					smart seq of setdb1b mt 1		strain:missing\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:missing\|dev stage:96hpf\|collection date:missing\|geo loc name:missing\|sex:pooled male and female\|tissue:hematopoietic stem and progenitor cell\|replicate:replicate = biological replicate 1\|id</u><u>:8</u><u>\|BioSampleModel:Model organism or animal									smart seq of setdb1b mt 1	smart seq of setdb1b mt 1	smart seq of setdb1b mt 1	smart seq of setdb1b mt of replicate 1		RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485121			smart-seq of setdb1b mt_1_R1.fastq.gz.gz smart-seq of setdb1b mt_1_R2.fastq.gz.gz	fastq fastq	9537788700.0	31792629.0	smart seq of setdb1b mt 1 R1.fastq.gz.gz	0:150 1:150	A:3044433376;C:1450924984;G:2142347814;T:2900047705;N:34821	150	150	3044433376	1450924984	2142347814	2900047705	34821	SRX23343657	SRS20205510	SRA1789215	East China Normal University\|Institute of Biomedical Sciences	East China Normal University	2	0.74808	0.79354	0.21148	0.22263	0.87405	0.87545	0.58431	0.58836	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-01-22	Larval	Larval	Blood	Hematopoietic System
30068	30068	SRR27676307	SRX23343656	SRS20205509	SRP485121	PRJNA1067443	RNA seq&smart seq&CUT TAG	PRJNA1067443	Other	RNA seq&smart seq&CUT TAG					smart seq of setdb1b control 2		strain:missing\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:missing\|dev stage:96hpf\|collection date:missing\|geo loc name:missing\|sex:pooled male and female\|tissue:hematopoietic stem and progenitor cell\|replicate:replicate = biological replicate 2\|id</u><u>:7</u><u>\|BioSampleModel:Model organism or animal									smart seq of setdb1b control 2	smart seq of setdb1b control 2	smart seq of setdb1b control 2	smart seq of setdb1b control of replicate 2		RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485121			smart-seq of setdb1b control_2_R1.fastq.gz.gz smart-seq of setdb1b control_2_R2.fastq.gz.gz	fastq fastq	7963596600.0	26545322.0	smart seq of setdb1b control 2 R1.fastq.gz.gz	0:150 1:150	A:2522387513;C:1217203824;G:1776725064;T:2447251088;N:29111	150	150	2522387513	1217203824	1776725064	2447251088	29111	SRX23343656	SRS20205509	SRA1789215	East China Normal University\|Institute of Biomedical Sciences	East China Normal University	2	0.77121	0.80578	0.22631	0.23757	0.85953	0.86298	0.58219	0.58387	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-01-22	Larval	Larval	Blood	Hematopoietic System
30069	30069	SRR27676308	SRX23343655	SRS20205508	SRP485121	PRJNA1067443	RNA seq&smart seq&CUT TAG	PRJNA1067443	Other	RNA seq&smart seq&CUT TAG					smart seq of setdb1b control 1		strain:missing\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:missing\|dev stage:96hpf\|collection date:missing\|geo loc name:missing\|sex:pooled male and female\|tissue:hematopoietic stem and progenitor cell\|replicate:replicate = biological replicate 1\|id</u><u>:6</u><u>\|BioSampleModel:Model organism or animal									smart seq of setdb1b control 1	smart seq of setdb1b control 1	smart seq of setdb1b control 1	smart seq of setdb1b control of replicate 1		RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485121			smart-seq of setdb1b control_1_R2.fastq.gz.gz smart-seq of setdb1b control_1_R1.fastq.gz.gz	fastq fastq	11867370900.0	39557903.0	smart seq of setdb1b control 1 R1.fastq.gz.gz	0:150 1:150	A:3969636478;C:1678555005;G:2520767064;T:3698368678;N:43675	150	150	3969636478	1678555005	2520767064	3698368678	43675	SRX23343655	SRS20205508	SRA1789215	East China Normal University\|Institute of Biomedical Sciences	East China Normal University	2	0.73517	0.73836	0.23036	0.23129	0.86407	0.86675	0.59652	0.59533	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-01-22	Larval	Larval	Blood	Hematopoietic System
30070	30070	SRR27676309	SRX23343654	SRS20205505	SRP485121	PRJNA1067443	RNA seq&smart seq&CUT TAG	PRJNA1067443	Other	RNA seq&smart seq&CUT TAG					RNA seq of atf7ip mt 2		strain:missing\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:missing\|dev stage:72hpf\|collection date:missing\|geo loc name:missing\|sex:pooled male and female\|tissue:hematopoietic stem and progenitor cell\|replicate:replicate = biological replicate 2\|id</u><u>:5</u><u>\|BioSampleModel:Model organism or animal									mRNAseq of atf7ip mt	RNA seq of atf7ip mt 2	RNA seq of atf7ip mt 2	mRNAseq of atf7ip mt of replicate 2		RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485121			RNA-seq of atf7ip mt_2_R2.fastq.gz.gz RNA-seq of atf7ip mt_2_R1.fastq.gz.gz	fastq fastq	2881485000.0	9604950.0	RNA seq of atf7ip mt 2 R1.fastq.gz.gz	0:150 1:150	A:714870764;C:672086586;G:819085358;T:675370688;N:71604	150	150	714870764	672086586	819085358	675370688	71604	SRX23343654	SRS20205505	SRA1789215	East China Normal University\|Institute of Biomedical Sciences	East China Normal University	2	0.95105	0.94782	0.0877	0.08683	0.67838	0.68085	0.4943	0.49308	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-01-22	Larval	Larval	Blood	Hematopoietic System
30071	30071	SRR27676310	SRX23343653	SRS20205506	SRP485121	PRJNA1067443	RNA seq&smart seq&CUT TAG	PRJNA1067443	Other	RNA seq&smart seq&CUT TAG					RNA seq of atf7ip mt 1		strain:missing\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:missing\|dev stage:72hpf\|collection date:missing\|geo loc name:missing\|sex:pooled male and female\|tissue:hematopoietic stem and progenitor cell\|replicate:replicate = biological replicate 1\|id</u><u>:4</u><u>\|BioSampleModel:Model organism or animal									mRNAseq of atf7ip mt	RNA seq of atf7ip mt 1	RNA seq of atf7ip mt 1	mRNAseq of atf7ip mt of replicate 1		RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485121			RNA-seq of atf7ip mt_1_R2.fastq.gz.gz RNA-seq of atf7ip mt_1_R1.fastq.gz.gz	fastq fastq	5215476900.0	17384923.0	RNA seq of atf7ip mt 1 R1.fastq.gz.gz	0:150 1:150	A:1305694077;C:1250588317;G:1437727006;T:1221425310;N:42190	150	150	1305694077	1250588317	1437727006	1221425310	42190	SRX23343653	SRS20205506	SRA1789215	East China Normal University\|Institute of Biomedical Sciences	East China Normal University	2	0.95459	0.9546	0.09418	0.0933	0.67353	0.67643	0.49356	0.49989	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-01-22	Larval	Larval	Blood	Hematopoietic System
30072	30072	SRR27676311	SRX23343652	SRS20205507	SRP485121	PRJNA1067443	RNA seq&smart seq&CUT TAG	PRJNA1067443	Other	RNA seq&smart seq&CUT TAG					RNA seq of atf7ip control 3		strain:missing\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:missing\|dev stage:72hpf\|collection date:missing\|geo loc name:missing\|sex:pooled male and female\|tissue:hematopoietic stem and progenitor cell\|replicate:replicate = biological replicate 3\|id</u><u>:3</u><u>\|BioSampleModel:Model organism or animal									mRNAseq of atf7ip control	RNA seq of atf7ip control 3	RNA seq of atf7ip control 3	mRNAseq of atf7ip control of replicate 3		RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485121			RNA-seq of atf7ip control_3_R2.fastq.gz.gz RNA-seq of atf7ip control_3_R1.fastq.gz.gz	fastq fastq	6742549200.0	22475164.0	RNA seq of atf7ip control 3 R1.fastq.gz.gz	0:150 1:150	A:1698977237;C:1657996046;G:1800441072;T:1584967439;N:167406	150	150	1698977237	1657996046	1800441072	1584967439	167406	SRX23343652	SRS20205507	SRA1789215	East China Normal University\|Institute of Biomedical Sciences	East China Normal University	2	0.96114	0.9601	0.05191	0.05152	0.69219	0.69398	0.48597	0.48633	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-01-22	Larval	Larval	Blood	Hematopoietic System
30073	30073	SRR27676312	SRX23343651	SRS20205504	SRP485121	PRJNA1067443	RNA seq&smart seq&CUT TAG	PRJNA1067443	Other	RNA seq&smart seq&CUT TAG					RNA seq of atf7ip control 2		strain:missing\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:missing\|dev stage:72hpf\|collection date:missing\|geo loc name:missing\|sex:pooled male and female\|tissue:hematopoietic stem and progenitor cell\|replicate:replicate = biological replicate 2\|id</u><u>:2</u><u>\|BioSampleModel:Model organism or animal									mRNAseq of atf7ip control	RNA seq of atf7ip control 2	RNA seq of atf7ip control 2	mRNAseq of atf7ip control of replicate 2		RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485121			RNA-seq of atf7ip control_2_R2.fastq.gz.gz RNA-seq of atf7ip control_2_R1.fastq.gz.gz	fastq fastq	6962540400.0	23208468.0	RNA seq of atf7ip control 2 R1.fastq.gz.gz	0:150 1:150	A:1794934846;C:1640272261;G:1855642638;T:1671491013;N:199642	150	150	1794934846	1640272261	1855642638	1671491013	199642	SRX23343651	SRS20205504	SRA1789215	East China Normal University\|Institute of Biomedical Sciences	East China Normal University	2	0.95531	0.95468	0.05949	0.05926	0.71019	0.71129	0.50401	0.50622	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-01-22	Larval	Larval	Blood	Hematopoietic System
30074	30074	SRR27676313	SRX23343650	SRS20205503	SRP485121	PRJNA1067443	RNA seq&smart seq&CUT TAG	PRJNA1067443	Other	RNA seq&smart seq&CUT TAG					RNA seq of atf7ip control 1		strain:missing\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:missing\|dev stage:72hpf\|collection date:missing\|geo loc name:missing\|sex:pooled male and female\|tissue:hematopoietic stem and progenitor cell\|replicate:replicate = biological replicate 1\|id</u><u>:1</u><u>\|BioSampleModel:Model organism or animal									mRNAseq of atf7ip control	RNA seq of atf7ip control 1	RNA seq of atf7ip control 1	mRNAseq of atf7ip control of replicate 1		RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485121			RNA-seq of atf7ip control_1_R1.fastq.gz.gz RNA-seq of atf7ip control_1_R2.fastq.gz.gz	fastq fastq	8543359800.0	28477866.0	RNA seq of atf7ip control 1 R1.fastq.gz.gz	0:150 1:150	A:2200058170;C:2049588985;G:2219737118;T:2073765388;N:210139	150	150	2200058170	2049588985	2219737118	2073765388	210139	SRX23343650	SRS20205503	SRA1789215	East China Normal University\|Institute of Biomedical Sciences	East China Normal University	2	0.96026	0.95618	0.05646	0.05613	0.68424	0.6856	0.48963	0.49334	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-01-22	Larval	Larval	Blood	Hematopoietic System
31522	31522	SRR28418937	SRX24023264	SRS20817617	SRP497230	PRJNA1090848	Reprogramming of 3D genome structure underlying HSPC development in zebrafish [RNA seq]	GSE262188	Transcriptome Analysis	Development of hematopoietic stem and progenitor cells HSPC is a multi staged complex process that conserved between zebrafish and mammals; however the mechanism underlying HSPC development is not fully understood. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision its dynamic and role in HSPC development is poorly investigated. Here we performed chromatin structure and multi omics dissection across different stages of HSPC developmental trajectory in zebrafish. Chromatin organization of zebrafish HSPC resemble mammalian cells with similar hierarchical structure and characteristics. We revealed the multi scale reorganization of 3D genome and its influence on transcriptional regulation and transition of cell function during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably PU.1 was identified as a potential factor mediating formation of promoter involved loops and regulating gene expression as well as HSPC function. Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factor involved in HSPC chromatin interactions which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision. Overall design: To comprehensively dissect 3D genome rearrangement and its relation to transcriptional changes of zebrafish HSPC we get RNA seq results from adult sample. Then conjoint analysis of RNA seq with other datas can reveal the function of transcriptional factors such as PU.1 .		pubmed:38886858		HPSC rep3 RNA seq 3month	GSM8159257		source name:hematopoietic stem cell\|tissue:hematopoietic stem cell\|cell line:TgCD41:GFP gata1:dsRed\|cell type:hematopoietic stem cell\|genotype:CD41+gata1 \|time:3month\|treatment:flow cytometry\|geo loc name:missing\|collection date:missing	HPSC rep3 RNA seq 3month	The library is evaluated by FastQC. Readswith mean quality score less than orequal to 30 are removed. Raw reads were trimmed and removed for adapter sequences by fatspv.0.23.2 withpaired end default parameters. Extremely short fragment with length less than or equal to 30bp were also removed. post filtering high quality reads were aligned to GRCz10 zebrafish genome using HISAT2 with default parameters. FeatureCounts wasused to quantify gene expression and obtain reads count. Fold changes in gene transcription levels were estimated using DESeq2.Enrichment analysis of gene function was performed in the Metascape platform. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample	hematopoietic stem cell		Briefly ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U RNase inhibitor 10 U dNTP mix 10 mM each SS III first strand buffer 1× DTT 5 mM betaine 1 M MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina		tissue:hematopoietic stem cell\|cell line:TgCD41:GFP gata1:dsRed\|cell type:hematopoietic stem cell\|genotype:CD41+gata1 \|time:3month\|treatment:flow cytometry	GSM8159257	GSM8159257: HPSC rep3 RNA seq 3month; Danio rerio; RNA Seq	GSM8159257 r1	GSM8159257	1	Briefly ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U RNase inhibitor 10 U dNTP mix 10 mM each SS III first strand buffer 1× DTT 5 mM betaine 1 M MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP497230		loader:fastq load.py	RNA-seq_Adult_HPSC_rep3_R1.fq.gz RNA-seq_Adult_HPSC_rep3_R2.fq.gz	fastq fastq	11621758500.0	38739195.0	GSM8159257 r1	0:150 1:150	A:3144084931;C:2632272493;G:2693165513;T:3151802925;N:432638	150	150	3144084931	2632272493	2693165513	3151802925	432638	SRX24023264	SRS20817617	SRA1831889	South China University of Technology	South China University of Technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-03-21	Adult	Adult	Blood	Hematopoietic System
31523	31523	SRR28418938	SRX24023263	SRS20817616	SRP497230	PRJNA1090848	Reprogramming of 3D genome structure underlying HSPC development in zebrafish [RNA seq]	GSE262188	Transcriptome Analysis	Development of hematopoietic stem and progenitor cells HSPC is a multi staged complex process that conserved between zebrafish and mammals; however the mechanism underlying HSPC development is not fully understood. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision its dynamic and role in HSPC development is poorly investigated. Here we performed chromatin structure and multi omics dissection across different stages of HSPC developmental trajectory in zebrafish. Chromatin organization of zebrafish HSPC resemble mammalian cells with similar hierarchical structure and characteristics. We revealed the multi scale reorganization of 3D genome and its influence on transcriptional regulation and transition of cell function during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably PU.1 was identified as a potential factor mediating formation of promoter involved loops and regulating gene expression as well as HSPC function. Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factor involved in HSPC chromatin interactions which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision. Overall design: To comprehensively dissect 3D genome rearrangement and its relation to transcriptional changes of zebrafish HSPC we get RNA seq results from adult sample. Then conjoint analysis of RNA seq with other datas can reveal the function of transcriptional factors such as PU.1 .		pubmed:38886858		HPSC rep2 RNA seq 3month	GSM8159256		source name:hematopoietic stem cell\|tissue:hematopoietic stem cell\|cell line:TgCD41:GFP gata1:dsRed\|cell type:hematopoietic stem cell\|genotype:CD41+gata1 \|time:3month\|treatment:flow cytometry\|geo loc name:missing\|collection date:missing	HPSC rep2 RNA seq 3month	The library is evaluated by FastQC. Readswith mean quality score less than orequal to 30 are removed. Raw reads were trimmed and removed for adapter sequences by fatspv.0.23.2 withpaired end default parameters. Extremely short fragment with length less than or equal to 30bp were also removed. post filtering high quality reads were aligned to GRCz10 zebrafish genome using HISAT2 with default parameters. FeatureCounts wasused to quantify gene expression and obtain reads count. Fold changes in gene transcription levels were estimated using DESeq2.Enrichment analysis of gene function was performed in the Metascape platform. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample	hematopoietic stem cell		Briefly ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U RNase inhibitor 10 U dNTP mix 10 mM each SS III first strand buffer 1× DTT 5 mM betaine 1 M MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina		tissue:hematopoietic stem cell\|cell line:TgCD41:GFP gata1:dsRed\|cell type:hematopoietic stem cell\|genotype:CD41+gata1 \|time:3month\|treatment:flow cytometry	GSM8159256	GSM8159256: HPSC rep2 RNA seq 3month; Danio rerio; RNA Seq	GSM8159256 r1	GSM8159256	1	Briefly ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U RNase inhibitor 10 U dNTP mix 10 mM each SS III first strand buffer 1× DTT 5 mM betaine 1 M MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP497230		loader:fastq load.py	RNA-seq_Adult_HPSC_rep2_R1.fq.gz RNA-seq_Adult_HPSC_rep2_R2.fq.gz	fastq fastq	9951217200.0	33170724.0	GSM8159256 r1	0:150 1:150	A:2755384814;C:2209586340;G:2237522365;T:2748523249;N:200432	150	150	2755384814	2209586340	2237522365	2748523249	200432	SRX24023263	SRS20817616	SRA1831889	South China University of Technology	South China University of Technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-03-21	Adult	Adult	Blood	Hematopoietic System
31524	31524	SRR28418939	SRX24023262	SRS20817615	SRP497230	PRJNA1090848	Reprogramming of 3D genome structure underlying HSPC development in zebrafish [RNA seq]	GSE262188	Transcriptome Analysis	Development of hematopoietic stem and progenitor cells HSPC is a multi staged complex process that conserved between zebrafish and mammals; however the mechanism underlying HSPC development is not fully understood. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision its dynamic and role in HSPC development is poorly investigated. Here we performed chromatin structure and multi omics dissection across different stages of HSPC developmental trajectory in zebrafish. Chromatin organization of zebrafish HSPC resemble mammalian cells with similar hierarchical structure and characteristics. We revealed the multi scale reorganization of 3D genome and its influence on transcriptional regulation and transition of cell function during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably PU.1 was identified as a potential factor mediating formation of promoter involved loops and regulating gene expression as well as HSPC function. Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factor involved in HSPC chromatin interactions which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision. Overall design: To comprehensively dissect 3D genome rearrangement and its relation to transcriptional changes of zebrafish HSPC we get RNA seq results from adult sample. Then conjoint analysis of RNA seq with other datas can reveal the function of transcriptional factors such as PU.1 .		pubmed:38886858		HPSC rep1 RNA seq 3month	GSM8159255		source name:hematopoietic stem cell\|tissue:hematopoietic stem cell\|cell line:TgCD41:GFP gata1:dsRed\|cell type:hematopoietic stem cell\|genotype:CD41+gata1 \|time:3month\|treatment:flow cytometry\|geo loc name:missing\|collection date:missing	HPSC rep1 RNA seq 3month	The library is evaluated by FastQC. Readswith mean quality score less than orequal to 30 are removed. Raw reads were trimmed and removed for adapter sequences by fatspv.0.23.2 withpaired end default parameters. Extremely short fragment with length less than or equal to 30bp were also removed. post filtering high quality reads were aligned to GRCz10 zebrafish genome using HISAT2 with default parameters. FeatureCounts wasused to quantify gene expression and obtain reads count. Fold changes in gene transcription levels were estimated using DESeq2.Enrichment analysis of gene function was performed in the Metascape platform. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample	hematopoietic stem cell		Briefly ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U RNase inhibitor 10 U dNTP mix 10 mM each SS III first strand buffer 1× DTT 5 mM betaine 1 M MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina		tissue:hematopoietic stem cell\|cell line:TgCD41:GFP gata1:dsRed\|cell type:hematopoietic stem cell\|genotype:CD41+gata1 \|time:3month\|treatment:flow cytometry	GSM8159255	GSM8159255: HPSC rep1 RNA seq 3month; Danio rerio; RNA Seq	GSM8159255 r1	GSM8159255	1	Briefly ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U RNase inhibitor 10 U dNTP mix 10 mM each SS III first strand buffer 1× DTT 5 mM betaine 1 M MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP497230		loader:fastq load.py	RNA-seq_Adult_HPSC_rep1_R1.fq.gz RNA-seq_Adult_HPSC_rep1_R2.fq.gz	fastq fastq	11096617200.0	36988724.0	GSM8159255 r1	0:150 1:150	A:3071303610;C:2460399138;G:2510824334;T:3053621175;N:468943	150	150	3071303610	2460399138	2510824334	3053621175	468943	SRX24023262	SRS20817615	SRA1831889	South China University of Technology	South China University of Technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-03-21	Adult	Adult	Blood	Hematopoietic System
33075	33075	SRR29654109	SRX25158199	SRS21848821	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3	GSM8369980		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100	GSM8369980	GSM8369980: Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3; Danio rerio; RNA Seq	GSM8369980 r1	GSM8369980	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_AMD_-016_cbc.fastq.gz	fastq	347162880.0	5786048.0	GSM8369980 r1	0:60	A:122562825;C:62219285;G:75539895;T:86775172;N:65703	60		122562825	62219285	75539895	86775172	65703	SRX25158199	SRS21848821	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33076	33076	SRR29654110	SRX25158199	SRS21848821	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3	GSM8369980		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100	GSM8369980	GSM8369980: Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3; Danio rerio; RNA Seq	GSM8369980 r1	GSM8369980	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_AMD_-016_cbc.fastq.gz	fastq	340954260.0	5682571.0	GSM8369980 r2	0:60	A:120149623;C:60854408;G:75192893;T:84703966;N:53370	60		120149623	60854408	75192893	84703966	53370	SRX25158199	SRS21848821	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33077	33077	SRR29654111	SRX25158199	SRS21848821	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3	GSM8369980		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100	GSM8369980	GSM8369980: Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3; Danio rerio; RNA Seq	GSM8369980 r1	GSM8369980	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_AMD_-016_cbc.fastq.gz	fastq	351749160.0	5862486.0	GSM8369980 r3	0:60	A:124352905;C:63078724;G:76291828;T:87988386;N:37317	60		124352905	63078724	76291828	87988386	37317	SRX25158199	SRS21848821	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33078	33078	SRR29654112	SRX25158199	SRS21848821	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3	GSM8369980		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100	GSM8369980	GSM8369980: Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 3; Danio rerio; RNA Seq	GSM8369980 r1	GSM8369980	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_AMD_-016_cbc.fastq.gz	fastq	345225720.0	5753762.0	GSM8369980 r4	0:60	A:121803902;C:61651407;G:75900430;T:85843789;N:26192	60		121803902	61651407	75900430	85843789	26192	SRX25158199	SRS21848821	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33079	33079	SRR29654113	SRX25158198	SRS21848820	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2	GSM8369979		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100	GSM8369979	GSM8369979: Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2; Danio rerio; RNA Seq	GSM8369979 r1	GSM8369979	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_AMD_-015_cbc.fastq.gz	fastq	159497640.0	2658294.0	GSM8369979 r1	0:60	A:55569742;C:28678683;G:33264744;T:41953354;N:31117	60		55569742	28678683	33264744	41953354	31117	SRX25158198	SRS21848820	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33080	33080	SRR29654114	SRX25158198	SRS21848820	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2	GSM8369979		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100	GSM8369979	GSM8369979: Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2; Danio rerio; RNA Seq	GSM8369979 r1	GSM8369979	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_AMD_-015_cbc.fastq.gz	fastq	156549240.0	2609154.0	GSM8369979 r2	0:60	A:54428858;C:28027289;G:33149650;T:40918247;N:25196	60		54428858	28027289	33149650	40918247	25196	SRX25158198	SRS21848820	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33081	33081	SRR29654115	SRX25158198	SRS21848820	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2	GSM8369979		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100	GSM8369979	GSM8369979: Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2; Danio rerio; RNA Seq	GSM8369979 r1	GSM8369979	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_AMD_-015_cbc.fastq.gz	fastq	161735280.0	2695588.0	GSM8369979 r3	0:60	A:56425187;C:29084972;G:33637112;T:42570603;N:17406	60		56425187	29084972	33637112	42570603	17406	SRX25158198	SRS21848820	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33082	33082	SRR29654116	SRX25158198	SRS21848820	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2	GSM8369979		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100	GSM8369979	GSM8369979: Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 2; Danio rerio; RNA Seq	GSM8369979 r1	GSM8369979	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_AMD_-015_cbc.fastq.gz	fastq	158621520.0	2643692.0	GSM8369979 r4	0:60	A:55213721;C:28430013;G:33462307;T:41503213;N:12266	60		55213721	28430013	33462307	41503213	12266	SRX25158198	SRS21848820	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33083	33083	SRR29654117	SRX25158197	SRS21848819	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1	GSM8369978		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100	GSM8369978	GSM8369978: Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1; Danio rerio; RNA Seq	GSM8369978 r1	GSM8369978	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_AMD_-011_cbc.fastq.gz	fastq	44363040.0	739384.0	GSM8369978 r1	0:60	A:17756825;C:7540147;G:9311367;T:9746444;N:8257	60		17756825	7540147	9311367	9746444	8257	SRX25158197	SRS21848819	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33084	33084	SRR29654118	SRX25158197	SRS21848819	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1	GSM8369978		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100	GSM8369978	GSM8369978: Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1; Danio rerio; RNA Seq	GSM8369978 r1	GSM8369978	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_AMD_-011_cbc.fastq.gz	fastq	43450800.0	724180.0	GSM8369978 r2	0:60	A:17376442;C:7355139;G:9244019;T:9468455;N:6745	60		17376442	7355139	9244019	9468455	6745	SRX25158197	SRS21848819	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33085	33085	SRR29654119	SRX25158197	SRS21848819	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1	GSM8369978		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100	GSM8369978	GSM8369978: Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1; Danio rerio; RNA Seq	GSM8369978 r1	GSM8369978	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_AMD_-011_cbc.fastq.gz	fastq	44795880.0	746598.0	GSM8369978 r3	0:60	A:17988707;C:7600964;G:9362568;T:9839285;N:4356	60		17988707	7600964	9362568	9839285	4356	SRX25158197	SRS21848819	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33086	33086	SRR29654120	SRX25158197	SRS21848819	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1	GSM8369978		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury AMD3100	GSM8369978	GSM8369978: Neutrophils mpx+ 8 xxx post injury AMD3100 biol rep 1; Danio rerio; RNA Seq	GSM8369978 r1	GSM8369978	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_AMD_-011_cbc.fastq.gz	fastq	44060940.0	734349.0	GSM8369978 r4	0:60	A:17608648;C:7492643;G:9327676;T:9628642;N:3331	60		17608648	7492643	9327676	9628642	3331	SRX25158197	SRS21848819	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33087	33087	SRR29654121	SRX25158196	SRS21848818	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ uninjured AMD3100 biol rep 3	GSM8369977		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured AMD3100 biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100	GSM8369977	GSM8369977: Neutrophils mpx+ uninjured AMD3100 biol rep 3; Danio rerio; RNA Seq	GSM8369977 r1	GSM8369977	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_AMD_-014_cbc.fastq.gz	fastq	115048140.0	1917469.0	GSM8369977 r1	0:60	A:41373215;C:21759509;G:21832537;T:30061744;N:21135	60		41373215	21759509	21832537	30061744	21135	SRX25158196	SRS21848818	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33088	33088	SRR29654122	SRX25158196	SRS21848818	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ uninjured AMD3100 biol rep 3	GSM8369977		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured AMD3100 biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100	GSM8369977	GSM8369977: Neutrophils mpx+ uninjured AMD3100 biol rep 3; Danio rerio; RNA Seq	GSM8369977 r1	GSM8369977	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_AMD_-014_cbc.fastq.gz	fastq	112845060.0	1880751.0	GSM8369977 r2	0:60	A:40482360;C:21287713;G:21750928;T:29306465;N:17594	60		40482360	21287713	21750928	29306465	17594	SRX25158196	SRS21848818	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33089	33089	SRR29654123	SRX25158196	SRS21848818	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ uninjured AMD3100 biol rep 3	GSM8369977		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured AMD3100 biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100	GSM8369977	GSM8369977: Neutrophils mpx+ uninjured AMD3100 biol rep 3; Danio rerio; RNA Seq	GSM8369977 r1	GSM8369977	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_AMD_-014_cbc.fastq.gz	fastq	116696580.0	1944943.0	GSM8369977 r3	0:60	A:42022776;C:22106040;G:22075778;T:30479513;N:12473	60		42022776	22106040	22075778	30479513	12473	SRX25158196	SRS21848818	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33090	33090	SRR29654124	SRX25158196	SRS21848818	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ uninjured AMD3100 biol rep 3	GSM8369977		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured AMD3100 biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100	GSM8369977	GSM8369977: Neutrophils mpx+ uninjured AMD3100 biol rep 3; Danio rerio; RNA Seq	GSM8369977 r1	GSM8369977	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_AMD_-014_cbc.fastq.gz	fastq	114334980.0	1905583.0	GSM8369977 r4	0:60	A:41132105;C:21578779;G:21934073;T:29681512;N:8511	60		41132105	21578779	21934073	29681512	8511	SRX25158196	SRS21848818	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33091	33091	SRR29654125	SRX25158195	SRS21848817	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ uninjured AMD3100 biol rep 2	GSM8369976		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured AMD3100 biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100	GSM8369976	GSM8369976: Neutrophils mpx+ uninjured AMD3100 biol rep 2; Danio rerio; RNA Seq	GSM8369976 r1	GSM8369976	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_AMD_-013_cbc.fastq.gz	fastq	354085380.0	5901423.0	GSM8369976 r1	0:60	A:124800871;C:65627966;G:72434440;T:91152029;N:70074	60		124800871	65627966	72434440	91152029	70074	SRX25158195	SRS21848817	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33092	33092	SRR29654126	SRX25158195	SRS21848817	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ uninjured AMD3100 biol rep 2	GSM8369976		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured AMD3100 biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100	GSM8369976	GSM8369976: Neutrophils mpx+ uninjured AMD3100 biol rep 2; Danio rerio; RNA Seq	GSM8369976 r1	GSM8369976	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_AMD_-013_cbc.fastq.gz	fastq	347250360.0	5787506.0	GSM8369976 r2	0:60	A:122147080;C:64042522;G:72135325;T:88869927;N:55506	60		122147080	64042522	72135325	88869927	55506	SRX25158195	SRS21848817	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33093	33093	SRR29654127	SRX25158195	SRS21848817	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ uninjured AMD3100 biol rep 2	GSM8369976		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured AMD3100 biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100	GSM8369976	GSM8369976: Neutrophils mpx+ uninjured AMD3100 biol rep 2; Danio rerio; RNA Seq	GSM8369976 r1	GSM8369976	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_AMD_-013_cbc.fastq.gz	fastq	358862580.0	5981043.0	GSM8369976 r3	0:60	A:126636264;C:66527902;G:73214426;T:92445348;N:38640	60		126636264	66527902	73214426	92445348	38640	SRX25158195	SRS21848817	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33094	33094	SRR29654128	SRX25158195	SRS21848817	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ uninjured AMD3100 biol rep 2	GSM8369976		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured AMD3100 biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100	GSM8369976	GSM8369976: Neutrophils mpx+ uninjured AMD3100 biol rep 2; Danio rerio; RNA Seq	GSM8369976 r1	GSM8369976	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_AMD_-013_cbc.fastq.gz	fastq	351843120.0	5864052.0	GSM8369976 r4	0:60	A:123921807;C:64956560;G:72828989;T:90107944;N:27820	60		123921807	64956560	72828989	90107944	27820	SRX25158195	SRS21848817	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33095	33095	SRR29654129	SRX25158194	SRS21848816	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ uninjured AMD3100 biol rep 1	GSM8369975		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured AMD3100 biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100	GSM8369975	GSM8369975: Neutrophils mpx+ uninjured AMD3100 biol rep 1; Danio rerio; RNA Seq	GSM8369975 r1	GSM8369975	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_AMD_-010_cbc.fastq.gz	fastq	100732380.0	1678873.0	GSM8369975 r1	0:60	A:37215898;C:18610797;G:18111317;T:26774380;N:19988	60		37215898	18610797	18111317	26774380	19988	SRX25158194	SRS21848816	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33096	33096	SRR29654130	SRX25158194	SRS21848816	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ uninjured AMD3100 biol rep 1	GSM8369975		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured AMD3100 biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100	GSM8369975	GSM8369975: Neutrophils mpx+ uninjured AMD3100 biol rep 1; Danio rerio; RNA Seq	GSM8369975 r1	GSM8369975	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_AMD_-010_cbc.fastq.gz	fastq	98830860.0	1647181.0	GSM8369975 r2	0:60	A:36388012;C:18195984;G:18122717;T:26108692;N:15455	60		36388012	18195984	18122717	26108692	15455	SRX25158194	SRS21848816	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33097	33097	SRR29654131	SRX25158194	SRS21848816	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ uninjured AMD3100 biol rep 1	GSM8369975		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured AMD3100 biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100	GSM8369975	GSM8369975: Neutrophils mpx+ uninjured AMD3100 biol rep 1; Danio rerio; RNA Seq	GSM8369975 r1	GSM8369975	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_AMD_-010_cbc.fastq.gz	fastq	102277560.0	1704626.0	GSM8369975 r3	0:60	A:37811843;C:18928051;G:18347174;T:27179477;N:11015	60		37811843	18928051	18347174	27179477	11015	SRX25158194	SRS21848816	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33098	33098	SRR29654132	SRX25158194	SRS21848816	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ uninjured AMD3100 biol rep 1	GSM8369975		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured AMD3100 biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured AMD3100	GSM8369975	GSM8369975: Neutrophils mpx+ uninjured AMD3100 biol rep 1; Danio rerio; RNA Seq	GSM8369975 r1	GSM8369975	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_AMD_-010_cbc.fastq.gz	fastq	100371840.0	1672864.0	GSM8369975 r4	0:60	A:37032383;C:18500721;G:18308236;T:26522753;N:7747	60		37032383	18500721	18308236	26522753	7747	SRX25158194	SRS21848816	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33099	33099	SRR29654133	SRX25158193	SRS21848815	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3	GSM8369974		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO	GSM8369974	GSM8369974: Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3; Danio rerio; RNA Seq	GSM8369974 r1	GSM8369974	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_DMSO_-008_cbc.fastq.gz	fastq	161717520.0	2695292.0	GSM8369974 r1	0:60	A:58227035;C:29120167;G:33153372;T:41186362;N:30584	60		58227035	29120167	33153372	41186362	30584	SRX25158193	SRS21848815	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33100	33100	SRR29654134	SRX25158193	SRS21848815	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3	GSM8369974		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO	GSM8369974	GSM8369974: Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3; Danio rerio; RNA Seq	GSM8369974 r1	GSM8369974	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_DMSO_-008_cbc.fastq.gz	fastq	158810460.0	2646841.0	GSM8369974 r2	0:60	A:57059029;C:28475827;G:33090143;T:40160441;N:25020	60		57059029	28475827	33090143	40160441	25020	SRX25158193	SRS21848815	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33101	33101	SRR29654135	SRX25158193	SRS21848815	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3	GSM8369974		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO	GSM8369974	GSM8369974: Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3; Danio rerio; RNA Seq	GSM8369974 r1	GSM8369974	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_DMSO_-008_cbc.fastq.gz	fastq	164136600.0	2735610.0	GSM8369974 r3	0:60	A:59164760;C:29564845;G:33567677;T:41822336;N:16982	60		59164760	29564845	33567677	41822336	16982	SRX25158193	SRS21848815	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33102	33102	SRR29654136	SRX25158193	SRS21848815	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3	GSM8369974		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO	GSM8369974	GSM8369974: Neutrophils mpx+ 8 xxx post injury DMSO biol rep 3; Danio rerio; RNA Seq	GSM8369974 r1	GSM8369974	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_DMSO_-008_cbc.fastq.gz	fastq	160939740.0	2682329.0	GSM8369974 r4	0:60	A:57905646;C:28872433;G:33402085;T:40746636;N:12940	60		57905646	28872433	33402085	40746636	12940	SRX25158193	SRS21848815	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33103	33103	SRR29654137	SRX25158192	SRS21848814	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2	GSM8369973		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO	GSM8369973	GSM8369973: Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2; Danio rerio; RNA Seq	GSM8369973 r1	GSM8369973	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_DMSO_-005_cbc.fastq.gz	fastq	294896760.0	4914946.0	GSM8369973 r1	0:60	A:113302890;C:53832811;G:54274745;T:73429183;N:57131	60		113302890	53832811	54274745	73429183	57131	SRX25158192	SRS21848814	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33104	33104	SRR29654138	SRX25158192	SRS21848814	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2	GSM8369973		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO	GSM8369973	GSM8369973: Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2; Danio rerio; RNA Seq	GSM8369973 r1	GSM8369973	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_DMSO_-005_cbc.fastq.gz	fastq	289658820.0	4827647.0	GSM8369973 r2	0:60	A:111138289;C:52646716;G:54190664;T:71637241;N:45910	60		111138289	52646716	54190664	71637241	45910	SRX25158192	SRS21848814	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33105	33105	SRR29654139	SRX25158192	SRS21848814	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2	GSM8369973		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO	GSM8369973	GSM8369973: Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2; Danio rerio; RNA Seq	GSM8369973 r1	GSM8369973	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_DMSO_-005_cbc.fastq.gz	fastq	299290800.0	4988180.0	GSM8369973 r3	0:60	A:115247052;C:54662821;G:54854607;T:74494831;N:31489	60		115247052	54662821	54854607	74494831	31489	SRX25158192	SRS21848814	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33106	33106	SRR29654140	SRX25158192	SRS21848814	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2	GSM8369973		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO	GSM8369973	GSM8369973: Neutrophils mpx+ 8 xxx post injury DMSO biol rep 2; Danio rerio; RNA Seq	GSM8369973 r1	GSM8369973	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_DMSO_-005_cbc.fastq.gz	fastq	294091920.0	4901532.0	GSM8369973 r4	0:60	A:113032051;C:53520496;G:54754695;T:72762244;N:22434	60		113032051	53520496	54754695	72762244	22434	SRX25158192	SRS21848814	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33107	33107	SRR29654141	SRX25158191	SRS21848813	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1	GSM8369972		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO	GSM8369972	GSM8369972: Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1; Danio rerio; RNA Seq	GSM8369972 r1	GSM8369972	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_DMSO_-004_cbc.fastq.gz	fastq	79542600.0	1325710.0	GSM8369972 r1	0:60	A:29052800;C:15106261;G:15344010;T:20023888;N:15641	60		29052800	15106261	15344010	20023888	15641	SRX25158191	SRS21848813	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33108	33108	SRR29654142	SRX25158191	SRS21848813	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1	GSM8369972		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO	GSM8369972	GSM8369972: Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1; Danio rerio; RNA Seq	GSM8369972 r1	GSM8369972	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_DMSO_-004_cbc.fastq.gz	fastq	78150840.0	1302514.0	GSM8369972 r2	0:60	A:28490299;C:14795977;G:15298357;T:19554765;N:11442	60		28490299	14795977	15298357	19554765	11442	SRX25158191	SRS21848813	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33109	33109	SRR29654143	SRX25158191	SRS21848813	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1	GSM8369972		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO	GSM8369972	GSM8369972: Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1; Danio rerio; RNA Seq	GSM8369972 r1	GSM8369972	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_DMSO_-004_cbc.fastq.gz	fastq	80719140.0	1345319.0	GSM8369972 r3	0:60	A:29548150;C:15350378;G:15486892;T:20325654;N:8066	60		29548150	15350378	15486892	20325654	8066	SRX25158191	SRS21848813	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33110	33110	SRR29654144	SRX25158191	SRS21848813	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1	GSM8369972		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:8 xxx post injury DMSO	GSM8369972	GSM8369972: Neutrophils mpx+ 8 xxx post injury DMSO biol rep 1; Danio rerio; RNA Seq	GSM8369972 r1	GSM8369972	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_DMSO_-004_cbc.fastq.gz	fastq	79070760.0	1317846.0	GSM8369972 r4	0:60	A:28874779;C:14986197;G:15407453;T:19795922;N:6409	60		28874779	14986197	15407453	19795922	6409	SRX25158191	SRS21848813	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33111	33111	SRR29654145	SRX25158190	SRS21848812	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ uninjured DMSO biol rep 3	GSM8369971		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured DMSO biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO	GSM8369971	GSM8369971: Neutrophils mpx+ uninjured DMSO biol rep 3; Danio rerio; RNA Seq	GSM8369971 r1	GSM8369971	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_DMSO_-009_cbc.fastq.gz	fastq	182391600.0	3039860.0	GSM8369971 r1	0:60	A:65842196;C:33929963;G:37226765;T:45358269;N:34407	60		65842196	33929963	37226765	45358269	34407	SRX25158190	SRS21848812	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33112	33112	SRR29654146	SRX25158190	SRS21848812	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ uninjured DMSO biol rep 3	GSM8369971		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured DMSO biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO	GSM8369971	GSM8369971: Neutrophils mpx+ uninjured DMSO biol rep 3; Danio rerio; RNA Seq	GSM8369971 r1	GSM8369971	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_DMSO_-009_cbc.fastq.gz	fastq	179081640.0	2984694.0	GSM8369971 r2	0:60	A:64544585;C:33163305;G:37078756;T:44266486;N:28508	60		64544585	33163305	37078756	44266486	28508	SRX25158190	SRS21848812	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33113	33113	SRR29654147	SRX25158190	SRS21848812	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ uninjured DMSO biol rep 3	GSM8369971		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured DMSO biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO	GSM8369971	GSM8369971: Neutrophils mpx+ uninjured DMSO biol rep 3; Danio rerio; RNA Seq	GSM8369971 r1	GSM8369971	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_DMSO_-009_cbc.fastq.gz	fastq	185068740.0	3084479.0	GSM8369971 r3	0:60	A:66919946;C:34450944;G:37652300;T:46025841;N:19709	60		66919946	34450944	37652300	46025841	19709	SRX25158190	SRS21848812	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System
33114	33114	SRR29654148	SRX25158190	SRS21848812	SRP517033	PRJNA1129880	Neutrophil immune profile guides spinal cord regeneration in zebrafish	GSE271113	Transcriptome Analysis	Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet their role in the repair process particularly in a regenerative context remains largely unknown. Here we show that promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether these findings provide new insights into the role of neutrophils in spinal cord regeneration emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100 and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT Portugal		pubmed:38925414		Neutrophils mpx+ uninjured DMSO biol rep 3	GSM8369971		tissue:Neutrophils mpx:GFP+\|cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO\|geo loc name:missing\|collection date:missing	Neutrophils mpx+ uninjured DMSO biol rep 3	Libraries were paired end sequenced on a Nextseq 500 Illumina high output with a 1x75 bp Illumina Kit Read 1: 26 cycles index read: 6 cycles Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script	Neutrophils mpx:GFP+	At 3 dpf larvae were anesthetized in 0.5 mM tricaine. Subsequenclty the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue	cell type:Neutrophils mpx:GFP+\|treatment:uninjured DMSO	GSM8369971	GSM8369971: Neutrophils mpx+ uninjured DMSO biol rep 3; Danio rerio; RNA Seq	GSM8369971 r1	GSM8369971	1	Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV 15 mM HEPES 25 mM D Glucose 2% goat serum in HBSS without xxx and calcium incubated at 28.5ºC shaking at 300 rpm and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP517033			IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_DMSO_-009_cbc.fastq.gz	fastq	181507740.0	3025129.0	GSM8369971 r4	0:60	A:65513514;C:33675079;G:37432606;T:44872485;N:14056	60		65513514	33675079	37432606	44872485	14056	SRX25158190	SRS21848812	SRA1913211	Instituto de Medicina Molecular	Instituto de Medicina Molecular												B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Portugal	2024-06-29	Larval	Larval	Blood	Hematopoietic System

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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");;