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.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.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.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
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,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,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,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,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,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,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,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,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,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,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,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
30066,SRR27676305,SRX23343658,SRS20205511,SRP485121,PRJNA1067443,RNA seq&smart seq&CUT TAG,PRJNA1067443,Other,RNA seq&amp;smart seq&amp;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,SRR27676306,SRX23343657,SRS20205510,SRP485121,PRJNA1067443,RNA seq&smart seq&CUT TAG,PRJNA1067443,Other,RNA seq&amp;smart seq&amp;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,SRR27676307,SRX23343656,SRS20205509,SRP485121,PRJNA1067443,RNA seq&smart seq&CUT TAG,PRJNA1067443,Other,RNA seq&amp;smart seq&amp;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,SRR27676308,SRX23343655,SRS20205508,SRP485121,PRJNA1067443,RNA seq&smart seq&CUT TAG,PRJNA1067443,Other,RNA seq&amp;smart seq&amp;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,SRR27676309,SRX23343654,SRS20205505,SRP485121,PRJNA1067443,RNA seq&smart seq&CUT TAG,PRJNA1067443,Other,RNA seq&amp;smart seq&amp;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,SRR27676310,SRX23343653,SRS20205506,SRP485121,PRJNA1067443,RNA seq&smart seq&CUT TAG,PRJNA1067443,Other,RNA seq&amp;smart seq&amp;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,SRR27676311,SRX23343652,SRS20205507,SRP485121,PRJNA1067443,RNA seq&smart seq&CUT TAG,PRJNA1067443,Other,RNA seq&amp;smart seq&amp;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,SRR27676312,SRX23343651,SRS20205504,SRP485121,PRJNA1067443,RNA seq&smart seq&CUT TAG,PRJNA1067443,Other,RNA seq&amp;smart seq&amp;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,SRR27676313,SRX23343650,SRS20205503,SRP485121,PRJNA1067443,RNA seq&smart seq&CUT TAG,PRJNA1067443,Other,RNA seq&amp;smart seq&amp;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
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,SRR29654148,SRX25158190,SRS21848812,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  DMSO  biol rep 3,GSM8369971,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  DMSO  biol rep 3,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO,GSM8369971,GSM8369971: Neutrophils mpx+  uninjured  DMSO  biol rep 3; Danio rerio; RNA Seq,GSM8369971 r1,GSM8369971,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_DMSO_-009_cbc.fastq.gz,fastq,181507740.0,3025129.0,GSM8369971 r4,0:60,A:65513514;C:33675079;G:37432606;T:44872485;N:14056,60,,,,65513514,33675079,37432606,44872485,14056,SRX25158190,SRS21848812,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33115,SRR29654149,SRX25158189,SRS21848811,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  DMSO  biol rep 2,GSM8369970,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  DMSO  biol rep 2,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO,GSM8369970,GSM8369970: Neutrophils mpx+  uninjured  DMSO  biol rep 2; Danio rerio; RNA Seq,GSM8369970 r1,GSM8369970,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_DMSO_-006_cbc.fastq.gz,fastq,45794760.0,763246.0,GSM8369970 r1,0:60,A:16928569;C:8492491;G:9006326;T:11358172;N:9202,60,,,,16928569,8492491,9006326,11358172,9202,SRX25158189,SRS21848811,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33116,SRR29654150,SRX25158189,SRS21848811,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  DMSO  biol rep 2,GSM8369970,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  DMSO  biol rep 2,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO,GSM8369970,GSM8369970: Neutrophils mpx+  uninjured  DMSO  biol rep 2; Danio rerio; RNA Seq,GSM8369970 r1,GSM8369970,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_DMSO_-006_cbc.fastq.gz,fastq,45009960.0,750166.0,GSM8369970 r2,0:60,A:16608407;C:8309766;G:8990622;T:11094414;N:6751,60,,,,16608407,8309766,8990622,11094414,6751,SRX25158189,SRS21848811,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33117,SRR29654151,SRX25158189,SRS21848811,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  DMSO  biol rep 2,GSM8369970,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  DMSO  biol rep 2,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO,GSM8369970,GSM8369970: Neutrophils mpx+  uninjured  DMSO  biol rep 2; Danio rerio; RNA Seq,GSM8369970 r1,GSM8369970,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_DMSO_-006_cbc.fastq.gz,fastq,46565880.0,776098.0,GSM8369970 r3,0:60,A:17217451;C:8640544;G:9146095;T:11557146;N:4644,60,,,,17217451,8640544,9146095,11557146,4644,SRX25158189,SRS21848811,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33118,SRR29654152,SRX25158189,SRS21848811,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  DMSO  biol rep 2,GSM8369970,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  DMSO  biol rep 2,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO,GSM8369970,GSM8369970: Neutrophils mpx+  uninjured  DMSO  biol rep 2; Danio rerio; RNA Seq,GSM8369970 r1,GSM8369970,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_DMSO_-006_cbc.fastq.gz,fastq,45624660.0,760411.0,GSM8369970 r4,0:60,A:16852187;C:8431444;G:9090234;T:11246907;N:3888,60,,,,16852187,8431444,9090234,11246907,3888,SRX25158189,SRS21848811,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33119,SRR29654153,SRX25158188,SRS21848810,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  DMSO  biol rep 1,GSM8369969,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  DMSO  biol rep 1,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO,GSM8369969,GSM8369969: Neutrophils mpx+  uninjured  DMSO  biol rep 1; Danio rerio; RNA Seq,GSM8369969 r1,GSM8369969,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_DMSO_-003_cbc.fastq.gz,fastq,55867380.0,931123.0,GSM8369969 r1,0:60,A:20680346;C:10254613;G:10895370;T:14026951;N:10100,60,,,,20680346,10254613,10895370,14026951,10100,SRX25158188,SRS21848810,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33120,SRR29654154,SRX25158188,SRS21848810,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  DMSO  biol rep 1,GSM8369969,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  DMSO  biol rep 1,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO,GSM8369969,GSM8369969: Neutrophils mpx+  uninjured  DMSO  biol rep 1; Danio rerio; RNA Seq,GSM8369969 r1,GSM8369969,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_DMSO_-003_cbc.fastq.gz,fastq,54889080.0,914818.0,GSM8369969 r2,0:60,A:20264110;C:10026239;G:10861715;T:13728039;N:8977,60,,,,20264110,10026239,10861715,13728039,8977,SRX25158188,SRS21848810,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33121,SRR29654155,SRX25158188,SRS21848810,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  DMSO  biol rep 1,GSM8369969,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  DMSO  biol rep 1,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO,GSM8369969,GSM8369969: Neutrophils mpx+  uninjured  DMSO  biol rep 1; Danio rerio; RNA Seq,GSM8369969 r1,GSM8369969,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_DMSO_-003_cbc.fastq.gz,fastq,56764440.0,946074.0,GSM8369969 r3,0:60,A:21036899;C:10416984;G:11027830;T:14275499;N:7228,60,,,,21036899,10416984,11027830,14275499,7228,SRX25158188,SRS21848810,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33122,SRR29654156,SRX25158188,SRS21848810,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  DMSO  biol rep 1,GSM8369969,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  DMSO  biol rep 1,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO,GSM8369969,GSM8369969: Neutrophils mpx+  uninjured  DMSO  biol rep 1; Danio rerio; RNA Seq,GSM8369969 r1,GSM8369969,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_DMSO_-003_cbc.fastq.gz,fastq,55531080.0,925518.0,GSM8369969 r4,0:60,A:20538193;C:10150017;G:10949669;T:13888674;N:4527,60,,,,20538193,10150017,10949669,13888674,4527,SRX25158188,SRS21848810,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
35485,SRR32834031,SRX28117245,SRS24473023,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  rag1 crispant  R848 treated,GSM8864273,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|genotype:rag1 mosaic mutant|treatment:Resiquimod R848 treated|geo loc name:missing|collection date:missing,mCherry cells  rag1 crispant  R848 treated,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells|genotype:rag1 mosaic mutant|treatment:Resiquimod R848 treated,GSM8864273,GSM8864273: mCherry cells  rag1 crispant  R848 treated; Danio rerio; RNA Seq,GSM8864273 r1,GSM8864273,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=Rag1 crispant with R848 S64 L005 R1 001.fastq.gz   read2PairFiles=Rag1 crispant with R848 S64 L005 R2 001.fastq.gz   read3PairFiles=Rag1 crispant with R848 S64 L005 I1 001.fastq.gz   read4PairFiles=Rag1 crispant with R848 S64 L005 I2 001.fastq.gz,Rag1_crispant_with_R848_S64_L005_I1_001.fastq.gz Rag1_crispant_with_R848_S64_L005_I2_001.fastq.gz Rag1_crispant_with_R848_S64_L005_R1_001.fastq.gz Rag1_crispant_with_R848_S64_L005_R2_001.fastq.gz,fastq fastq fastq fastq,51690121264.0,371871376.0,GSM8864273 r1,0:28 1:91 2:10 3:10,A:9268291738;C:7690563124;G:8398909329;T:8480309041;N:2221984,28,91,10,10,9268291738,7690563124,8398909329,8480309041,2221984,SRX28117245,SRS24473023,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35486,SRR32834032,SRX28117244,SRS24473025,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  slc24a5 crispant  R848 treated,GSM8864272,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|genotype:slc24a5 mosaic mutant|treatment:Resiquimod R848 treated|geo loc name:missing|collection date:missing,mCherry cells  slc24a5 crispant  R848 treated,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells|genotype:slc24a5 mosaic mutant|treatment:Resiquimod R848 treated,GSM8864272,GSM8864272: mCherry cells  slc24a5 crispant  R848 treated; Danio rerio; RNA Seq,GSM8864272 r1,GSM8864272,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=slc24a5 crispant with R848 S62 L005 R1 001.fastq.gz   read2PairFiles=slc24a5 crispant with R848 S62 L005 R2 001.fastq.gz   read3PairFiles=slc24a5 crispant with R848 S62 L005 I1 001.fastq.gz   read4PairFiles=slc24a5 crispant with R848 S62 L005 I2 001.fastq.gz,slc24a5_crispant_with_R848_S62_L005_I1_001.fastq.gz slc24a5_crispant_with_R848_S62_L005_I2_001.fastq.gz slc24a5_crispant_with_R848_S62_L005_R1_001.fastq.gz slc24a5_crispant_with_R848_S62_L005_R2_001.fastq.gz,fastq fastq fastq fastq,67359016638.0,484597242.0,GSM8864272 r1,0:28 1:91 2:10 3:10,A:12101967291;C:10017190111;G:10977547337;T:10998758556;N:2885727,28,91,10,10,12101967291,10017190111,10977547337,10998758556,2885727,SRX28117244,SRS24473025,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35487,SRR32834033,SRX28117243,SRS24473024,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  rag1 crispant,GSM8864271,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|genotype:rag1 mosaic mutant|geo loc name:missing|collection date:missing,mCherry cells  rag1 crispant,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells|genotype:rag1 mosaic mutant,GSM8864271,GSM8864271: mCherry cells  rag1 crispant; Danio rerio; RNA Seq,GSM8864271 r1,GSM8864271,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=Rag1 crispant S63 L005 R1 001.fastq.gz   read2PairFiles=Rag1 crispant S63 L005 R2 001.fastq.gz   read3PairFiles=Rag1 crispant S63 L005 I1 001.fastq.gz   read4PairFiles=Rag1 crispant S63 L005 I2 001.fastq.gz,Rag1_crispant_S63_L005_I1_001.fastq.gz Rag1_crispant_S63_L005_I2_001.fastq.gz Rag1_crispant_S63_L005_R1_001.fastq.gz Rag1_crispant_S63_L005_R2_001.fastq.gz,fastq fastq fastq fastq,40550115550.0,291727450.0,GSM8864271 r1,0:28 1:91 2:10 3:10,A:7262987235;C:6078752458;G:6639990009;T:6563701562;N:1766686,28,91,10,10,7262987235,6078752458,6639990009,6563701562,1766686,SRX28117243,SRS24473024,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35488,SRR32834034,SRX28117242,SRS24473022,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  slc24a5 crispant,GSM8864270,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|genotype:slc24a5 mosaic mutant|geo loc name:missing|collection date:missing,mCherry cells  slc24a5 crispant,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells|genotype:slc24a5 mosaic mutant,GSM8864270,GSM8864270: mCherry cells  slc24a5 crispant; Danio rerio; RNA Seq,GSM8864270 r1,GSM8864270,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=slc24a5 crispant S61 L005 R1 001.fastq.gz   read2PairFiles=slc24a5 crispant S61 L005 R2 001.fastq.gz   read3PairFiles=slc24a5 crispant S61 L005 I1 001.fastq.gz   read4PairFiles=slc24a5 crispant S61 L005 I2 001.fastq.gz,slc24a5_crispant_S61_L005_I1_001.fastq.gz slc24a5_crispant_S61_L005_I2_001.fastq.gz slc24a5_crispant_S61_L005_R1_001.fastq.gz slc24a5_crispant_S61_L005_R2_001.fastq.gz,fastq fastq fastq fastq,53500554564.0,384896076.0,GSM8864270 r1,0:28 1:91 2:10 3:10,A:9607899809;C:8061049626;G:8772491787;T:8581787300;N:2314394,28,91,10,10,9607899809,8061049626,8772491787,8581787300,2314394,SRX28117242,SRS24473022,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35489,SRR32834035,SRX28117241,SRS24473017,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  runx1 homozygous mutants,GSM8864269,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|genotype:runx1 homozygous|geo loc name:missing|collection date:missing,mCherry cells  runx1 homozygous mutants,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells|genotype:runx1 homozygous,GSM8864269,GSM8864269: mCherry cells  runx1 homozygous mutants; Danio rerio; RNA Seq,GSM8864269 r1,GSM8864269,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=Runx1 Homz Mutants earlyHSPC trace 6 dpf S2 L002 R1 001.fastq.gz   read2PairFiles=Runx1 Homz Mutants earlyHSPC trace 6 dpf S2 L002 R2 001.fastq.gz   read3PairFiles=Runx1 Homz Mutants earlyHSPC trace 6 dpf S2 L002 I1 001.fastq.gz   read4PairFiles=Runx1 Homz Mutants earlyHSPC trace 6 dpf S2 L002 I2 001.fastq.gz,Runx1_Homz_Mutants_earlyHSPC_trace_6_dpf_S2_L002_I1_001.fastq.gz Runx1_Homz_Mutants_earlyHSPC_trace_6_dpf_S2_L002_I2_001.fastq.gz Runx1_Homz_Mutants_earlyHSPC_trace_6_dpf_S2_L002_R1_001.fastq.gz Runx1_Homz_Mutants_earlyHSPC_trace_6_dpf_S2_L002_R2_001.fastq.gz,fastq fastq fastq fastq,27845512960.0,87017228.0,GSM8864269 r1,0:150 1:150 2:10 3:10,A:4012440512;C:2615250336;G:3042659166;T:3381797139;N:437047,150,150,10,10,4012440512,2615250336,3042659166,3381797139,437047,SRX28117241,SRS24473017,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35490,SRR32834036,SRX28117240,SRS24473018,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  sibling controls,GSM8864268,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|genotype:wild type or runx1 heterozygous|geo loc name:missing|collection date:missing,mCherry cells  sibling controls,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells|genotype:wild type or runx1 heterozygous,GSM8864268,GSM8864268: mCherry cells  sibling controls; Danio rerio; RNA Seq,GSM8864268 r1,GSM8864268,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=Sibling Control earlyHSPC trace 6 dpf S1 L002 R1 001.fastq.gz   read2PairFiles=Sibling Control earlyHSPC trace 6 dpf S1 L002 R2 001.fastq.gz   read3PairFiles=Sibling Control earlyHSPC trace 6 dpf S1 L002 I1 001.fastq.gz   read4PairFiles=Sibling Control earlyHSPC trace 6 dpf S1 L002 I2 001.fastq.gz,Sibling_Control_earlyHSPC_trace_6_dpf_S1_L002_I1_001.fastq.gz Sibling_Control_earlyHSPC_trace_6_dpf_S1_L002_I2_001.fastq.gz Sibling_Control_earlyHSPC_trace_6_dpf_S1_L002_R1_001.fastq.gz Sibling_Control_earlyHSPC_trace_6_dpf_S1_L002_R2_001.fastq.gz,fastq fastq fastq fastq,24953253760.0,77978918.0,GSM8864268 r1,0:150 1:150 2:10 3:10,A:3390875336;C:2571521800;G:2871954356;T:2862416982;N:69226,150,150,10,10,3390875336,2571521800,2871954356,2862416982,69226,SRX28117240,SRS24473018,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35491,SRR32834037,SRX28117239,SRS24473015,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  late HSPCs 10 dpf,GSM8864267,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells  late HSPCs 10 dpf,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells,GSM8864267,GSM8864267: mCherry cells  late HSPCs 10 dpf; Danio rerio; RNA Seq,GSM8864267 r1,GSM8864267,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=lateHSPC trace at 10dpf S1 L003 R1 001.fastq.gz   read2PairFiles=lateHSPC trace at 10dpf S1 L003 R2 001.fastq.gz   read3PairFiles=lateHSPC trace at 10dpf S1 L003 I1 001.fastq.gz   read4PairFiles=lateHSPC trace at 10dpf S1 L003 I2 001.fastq.gz,lateHSPC_trace_at_10dpf_S1_L003_I1_001.fastq.gz lateHSPC_trace_at_10dpf_S1_L003_I2_001.fastq.gz lateHSPC_trace_at_10dpf_S1_L003_R1_001.fastq.gz lateHSPC_trace_at_10dpf_S1_L003_R2_001.fastq.gz,fastq fastq fastq fastq,49750537600.0,155470430.0,GSM8864267 r1,0:150 1:150 2:10 3:10,A:6695708919;C:5110107098;G:5648204020;T:5864962224;N:1582239,150,150,10,10,6695708919,5110107098,5648204020,5864962224,1582239,SRX28117239,SRS24473015,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35492,SRR32834038,SRX28117239,SRS24473015,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  late HSPCs 10 dpf,GSM8864267,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells  late HSPCs 10 dpf,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells,GSM8864267,GSM8864267: mCherry cells  late HSPCs 10 dpf; Danio rerio; RNA Seq,GSM8864267 r1,GSM8864267,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=lateHSPC trace at 10dpf S18 L002 R1 001.fastq.gz   read2PairFiles=lateHSPC trace at 10dpf S18 L002 R2 001.fastq.gz   read3PairFiles=lateHSPC trace at 10dpf S18 L002 I1 001.fastq.gz   read4PairFiles=lateHSPC trace at 10dpf S18 L002 I2 001.fastq.gz,lateHSPC_trace_at_10dpf_S18_L002_I1_001.fastq.gz lateHSPC_trace_at_10dpf_S18_L002_I2_001.fastq.gz lateHSPC_trace_at_10dpf_S18_L002_R1_001.fastq.gz lateHSPC_trace_at_10dpf_S18_L002_R2_001.fastq.gz,fastq fastq fastq fastq,3818546250.0,27670625.0,GSM8864267 r2,0:28 1:90 2:10 3:10,A:716133237;C:554493684;G:608989896;T:610460128;N:279305,28,90,10,10,716133237,554493684,608989896,610460128,279305,SRX28117239,SRS24473015,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35493,SRR32834039,SRX28117238,SRS24473019,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  late HSPCs 6 dpf,GSM8864266,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells  late HSPCs 6 dpf,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells,GSM8864266,GSM8864266: mCherry cells  late HSPCs 6 dpf; Danio rerio; RNA Seq,GSM8864266 r1,GSM8864266,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=lateHSPC trace at 6dpf S17 L002 R1 001.fastq.gz   read2PairFiles=lateHSPC trace at 6dpf S17 L002 R2 001.fastq.gz   read3PairFiles=lateHSPC trace at 6dpf S17 L002 I1 001.fastq.gz   read4PairFiles=lateHSPC trace at 6dpf S17 L002 I2 001.fastq.gz,lateHSPC_trace_at_6dpf_S17_L002_I1_001.fastq.gz lateHSPC_trace_at_6dpf_S17_L002_I2_001.fastq.gz lateHSPC_trace_at_6dpf_S17_L002_R1_001.fastq.gz lateHSPC_trace_at_6dpf_S17_L002_R2_001.fastq.gz,fastq fastq fastq fastq,12871712088.0,93273276.0,GSM8864266 r1,0:28 1:90 2:10 3:10,A:2421583617;C:1888963122;G:2078815965;T:2004213972;N:1018164,28,90,10,10,2421583617,1888963122,2078815965,2004213972,1018164,SRX28117238,SRS24473019,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35494,SRR32834040,SRX28117237,SRS24473014,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  late HSPCs 4 dpf,GSM8864265,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells  late HSPCs 4 dpf,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells,GSM8864265,GSM8864265: mCherry cells  late HSPCs 4 dpf; Danio rerio; RNA Seq,GSM8864265 r1,GSM8864265,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=lateHSPC trace at 4dpf S16 L002 R1 001.fastq.gz   read2PairFiles=lateHSPC trace at 4dpf S16 L002 R2 001.fastq.gz   read3PairFiles=lateHSPC trace at 4dpf S16 L002 I1 001.fastq.gz   read4PairFiles=lateHSPC trace at 4dpf S16 L002 I2 001.fastq.gz,lateHSPC_trace_at_4dpf_S16_L002_I1_001.fastq.gz lateHSPC_trace_at_4dpf_S16_L002_I2_001.fastq.gz lateHSPC_trace_at_4dpf_S16_L002_R1_001.fastq.gz lateHSPC_trace_at_4dpf_S16_L002_R2_001.fastq.gz,fastq fastq fastq fastq,11138275734.0,80712143.0,GSM8864265 r1,0:28 1:90 2:10 3:10,A:2022661838;C:1679042427;G:1720706851;T:1840857883;N:823871,28,90,10,10,2022661838,1679042427,1720706851,1840857883,823871,SRX28117237,SRS24473014,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35495,SRR32834041,SRX28117236,SRS24473016,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  mid HSPCs 10 dpf,GSM8864264,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells  mid HSPCs 10 dpf,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells,GSM8864264,GSM8864264: mCherry cells  mid HSPCs 10 dpf; Danio rerio; RNA Seq,GSM8864264 r1,GSM8864264,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=midHSPC 10dpf S1 L001 R1 001.fastq.gz   read2PairFiles=midHSPC 10dpf S1 L001 R2 001.fastq.gz   read3PairFiles=midHSPC 10dpf S1 L001 I1 001.fastq.gz   read4PairFiles=midHSPC 10dpf S1 L001 I2 001.fastq.gz,midHSPC_10dpf_S1_L001_I1_001.fastq.gz midHSPC_10dpf_S1_L001_I2_001.fastq.gz midHSPC_10dpf_S1_L001_R1_001.fastq.gz midHSPC_10dpf_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,211217834240.0,660055732.0,GSM8864264 r1,0:150 1:150 2:10 3:10,A:28426769480;C:22300370613;G:24520861829;T:23758933345;N:1424533,150,150,10,10,28426769480,22300370613,24520861829,23758933345,1424533,SRX28117236,SRS24473016,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35496,SRR32834042,SRX28117235,SRS24473020,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  mid HSPCs 6 dpf,GSM8864263,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells  mid HSPCs 6 dpf,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells,GSM8864263,GSM8864263: mCherry cells  mid HSPCs 6 dpf; Danio rerio; RNA Seq,GSM8864263 r1,GSM8864263,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=midHSPC 6dpf S1 L001 R1 001.fastq.gz   read2PairFiles=midHSPC 6dpf S1 L001 R2 001.fastq.gz   read3PairFiles=midHSPC 6dpf S1 L001 I1 001.fastq.gz   read4PairFiles=midHSPC 6dpf S1 L001 I2 001.fastq.gz,midHSPC_6dpf_S1_L001_I1_001.fastq.gz midHSPC_6dpf_S1_L001_I2_001.fastq.gz midHSPC_6dpf_S1_L001_R1_001.fastq.gz midHSPC_6dpf_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,241173414720.0,753666921.0,GSM8864263 r1,,,,,,,,,,,,SRX28117235,SRS24473020,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,1,0.94667,,0.08748,,0.83881,,0.5015,,150,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35497,SRR32834043,SRX28117234,SRS24473021,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  mid HSPCs 3 dpf,GSM8864262,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells  mid HSPCs 3 dpf,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells,GSM8864262,GSM8864262: mCherry cells  mid HSPCs 3 dpf; Danio rerio; RNA Seq,GSM8864262 r1,GSM8864262,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=midHSPC 3dpf S6 L003 R1 001.fastq.gz   read2PairFiles=midHSPC 3dpf S6 L003 R2 001.fastq.gz   read3PairFiles=midHSPC 3dpf S6 L003 I1 001.fastq.gz   read4PairFiles=midHSPC 3dpf S6 L003 I2 001.fastq.gz,midHSPC_3dpf_S6_L003_I1_001.fastq.gz midHSPC_3dpf_S6_L003_I2_001.fastq.gz midHSPC_3dpf_S6_L003_R1_001.fastq.gz midHSPC_3dpf_S6_L003_R2_001.fastq.gz,fastq fastq fastq fastq,71933359680.0,224791749.0,GSM8864262 r1,0:150 1:150 2:10 3:10,A:9519625855;C:6982221178;G:8366028895;T:7767873072;N:1083013350,150,150,10,10,9519625855,6982221178,8366028895,7767873072,1083013350,SRX28117234,SRS24473021,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,1,0.78368,,0.08584,,0.82144,,0.50936,,150,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35498,SRR32834044,SRX28117233,SRS24473012,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  early HSPCs 10 dpf,GSM8864261,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells  early HSPCs 10 dpf,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells,GSM8864261,GSM8864261: mCherry cells  early HSPCs 10 dpf; Danio rerio; RNA Seq,GSM8864261 r1,GSM8864261,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=earlyHSPC 10dpf S1 L001 R1 001.fastq.gz   read2PairFiles=earlyHSPC 10dpf S1 L001 R2 001.fastq.gz   read3PairFiles=earlyHSPC 10dpf S1 L001 I1 001.fastq.gz   read4PairFiles=earlyHSPC 10dpf S1 L001 I2 001.fastq.gz,earlyHSPC_10dpf_S1_L001_I1_001.fastq.gz earlyHSPC_10dpf_S1_L001_I2_001.fastq.gz earlyHSPC_10dpf_S1_L001_R1_001.fastq.gz earlyHSPC_10dpf_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,267665197120.0,836453741.0,GSM8864261 r1,,,,,,,,,,,,SRX28117233,SRS24473012,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
35499,SRR32834045,SRX28117232,SRS24473013,SRP572644,PRJNA1241156,Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish,GSE292726,Transcriptome Analysis,Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis  hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs  we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave  we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly  embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment  HSPCs were labled with mCherry at 3 timepoints in development: either at 1  2  or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling  6 dpf  and 10 dpf. Experiment 2: for Runx1 mutants experiment  early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment  mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls  rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.,,,,mCherry cells  early HSPCs 6 dpf,GSM8864260,,tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing,mCherry cells  early HSPCs 6 dpf,For experiments 1 lineage tracing and 2 runx1 mutants  CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848  CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix,Hematopoietic & Immune Cells,The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,Larvae were maintained in standard conditions  at 28C,cell type:Hematopoietic & Immune Cells,GSM8864260,GSM8864260: mCherry cells  early HSPCs 6 dpf; Danio rerio; RNA Seq,GSM8864260 r1,GSM8864260,1,Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants  the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848  the Chromium Next GEM Single Cell three prime Kit v4 was used.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP572644,,loader:fastq load.py|options:  readTypes=TBTT   read1PairFiles=earlyHSPC 6dpf S1 L001 R1 001.fastq.gz   read2PairFiles=earlyHSPC 6dpf S1 L001 R2 001.fastq.gz   read3PairFiles=earlyHSPC 6dpf S1 L001 I1 001.fastq.gz   read4PairFiles=earlyHSPC 6dpf S1 L001 I2 001.fastq.gz,earlyHSPC_6dpf_S1_L001_I1_001.fastq.gz earlyHSPC_6dpf_S1_L001_I2_001.fastq.gz earlyHSPC_6dpf_S1_L001_R1_001.fastq.gz earlyHSPC_6dpf_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,234759123200.0,733622260.0,GSM8864260 r1,,,,,,,,,,,,SRX28117232,SRS24473013,SRA2098862,Albert Einstein College of Medicine,Albert Einstein College of Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-24,Larval,Larval,Blood,Hematopoietic System
36249,SRR34017907,SRX29213468,SRS25409913,SRP592701,PRJNA1278741,Single cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches [scRNA Seq],GSE300039,Transcriptome Analysis,Hematopoietic stem cells HSCs and more committed progenitors collectively referred to as HSPCs emerge from vessels during development  via Endothelial to Hematopoietic Transition EHT. Recently  using the zebrafish embryo  we showed that two EHT cell types emerge from the dorsal aorta  raising the question of their subsequent fate. To address this issue  we established a complex pipeline based on single cell photoconversion and transgenic lines to characterize the abilities of EHT cell progenies to conquer hematopoietic organs and to obtain their transcriptomic profiles. We show that the two EHT cell types lead to partly differentially fated cells  with significant differences in thymus colonization and T lymphoid lineage commitment. In addition  we investigated implantation of HSPCs in niches  with the support of HSPC signatures gata2b and cd34/podocalyxin  retrieved from our single cell datasets. This revealed  at unprecedented resolution  the homing of HSPCs in niches of entire early larvae  including the pronephros  the sub aortic and caudal regions  as well as the area contacting the supra intestinal artery. Our work provides new insights on fundamental aspects of HSPC fate acquisition  from their emergence to their homing in specific niches. Overall design: Single cell transcriptomics analysis of newly born hematopoietic stem and progenitor cells. This dataset comprises progenies of cells photoconverted at 2dpf and sorted by FACS at 5dpf  using the Tgkdrl:nls kikume transgenic line  as well as sorted FACS hematopoietic cells from transgenic reporter lines  namely from the Tgrunx1+23:eGFP and the outcross of the Tgcd41:eGFP and Tggata2b:RFP lines. Larvae were collected post dissection separating the rostral  anterior and posterior region along a transversal section at the posterior limit of the elongated yolk and at the posterior limit of the swim bladder  dissociation and sorting using a BD FACS AriaIII cell sorter. Progenies of photoconverted cells comprise progenies of single EHT photoconversion either EHT pol+ or EHT pol  or whole hemogenic endothelium photoconversion. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019.,,pubmed:40501392,,5 dpf hematopoietic zebrafish cells  session 2,GSM9052756,,tissue:sorted hematopoietic cells|cell type:sorted hematopoietic cells|geo loc name:missing|collection date:missing,5 dpf hematopoietic zebrafish cells  session 2,Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019 Assembly: zebrafish genome Lawson lab version 4.3.2. Supplementary files format and content: Tab separated value files,sorted hematopoietic cells,,Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al.  2018; Manoli and Driever  2012; Samsa et al.  2016. All steps were performed with cooled solutions 4°C  and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly  5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine  at a final concentration of 640 µg/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4°C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies  Cat#: 12605 010 for 10 min on ice  with gentle pipetting every 3 mins  first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g  before the TrypLE was removed and the cells were resuspended in 500 µl FACSmax medium Genlantis  Cat#: T200100. Ultimately  samples were passed through a 40 μm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 µl of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples  gating was done on SSC A vs. FSC A to collect cells  then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher  Cat#: D15106. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019. Briefly  a first step of reverse transcription RT SuperScript III  Thermo Fisher  Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT  primers were removed with an exonuclease ExoI NEB  Cat#: M0293L  and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit  NEB  Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit  NEB  Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher  Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher  Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase  Agilent  Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix  Roche Diagnostics  Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and ß actin  DNA quality control using a TapeStation  Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.,,cell type:sorted hematopoietic cells,GSM9052756,GSM9052756: 5 dpf hematopoietic zebrafish cells  session 2; Danio rerio; RNA Seq,GSM9052756 r1,GSM9052756,1,Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al.  2018; Manoli and Driever  2012; Samsa et al.  2016. All steps were performed with cooled solutions 4°C  and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly  5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine  at a final concentration of 640 µg/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4°C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies  Cat#: 12605 010 for 10 min on ice  with gentle pipetting every 3 mins  first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g  before the TrypLE was removed and the cells were resuspended in 500 µl FACSmax medium Genlantis  Cat#: T200100. Ultimately  samples were passed through a 40 μm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 µl of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples  gating was done on SSC A vs. FSC A to collect cells  then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher  Cat#: D15106. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019. Briefly  a first step of reverse transcription RT SuperScript III  Thermo Fisher  Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT  primers were removed with an exonuclease ExoI NEB  Cat#: M0293L  and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit  NEB  Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit  NEB  Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher  Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher  Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase  Agilent  Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix  Roche Diagnostics  Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and ß actin  DNA quality control using a TapeStation  Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP592701,,,TORCQ_2023_S0_L001_R1_001.fastq.gz TORCQ_2023_S0_L001_R2_001.fastq.gz,fastq fastq,9123251137.0,118483781.0,GSM9052756 r1,0:57 1:20,A:2003237489;C:1403878506;G:1540717140;T:1805684398;N:2369733604,57,20,,,2003237489,1403878506,1540717140,1805684398,2369733604,SRX29213468,SRS25409913,SRA2151098,Institut Pasteur,Institut Pasteur,,,,,,,,,,,,,,,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,marsseq,,France,2025-06-17,Larval,Larval,Blood,Hematopoietic System
36250,SRR34017908,SRX29213468,SRS25409913,SRP592701,PRJNA1278741,Single cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches [scRNA Seq],GSE300039,Transcriptome Analysis,Hematopoietic stem cells HSCs and more committed progenitors collectively referred to as HSPCs emerge from vessels during development  via Endothelial to Hematopoietic Transition EHT. Recently  using the zebrafish embryo  we showed that two EHT cell types emerge from the dorsal aorta  raising the question of their subsequent fate. To address this issue  we established a complex pipeline based on single cell photoconversion and transgenic lines to characterize the abilities of EHT cell progenies to conquer hematopoietic organs and to obtain their transcriptomic profiles. We show that the two EHT cell types lead to partly differentially fated cells  with significant differences in thymus colonization and T lymphoid lineage commitment. In addition  we investigated implantation of HSPCs in niches  with the support of HSPC signatures gata2b and cd34/podocalyxin  retrieved from our single cell datasets. This revealed  at unprecedented resolution  the homing of HSPCs in niches of entire early larvae  including the pronephros  the sub aortic and caudal regions  as well as the area contacting the supra intestinal artery. Our work provides new insights on fundamental aspects of HSPC fate acquisition  from their emergence to their homing in specific niches. Overall design: Single cell transcriptomics analysis of newly born hematopoietic stem and progenitor cells. This dataset comprises progenies of cells photoconverted at 2dpf and sorted by FACS at 5dpf  using the Tgkdrl:nls kikume transgenic line  as well as sorted FACS hematopoietic cells from transgenic reporter lines  namely from the Tgrunx1+23:eGFP and the outcross of the Tgcd41:eGFP and Tggata2b:RFP lines. Larvae were collected post dissection separating the rostral  anterior and posterior region along a transversal section at the posterior limit of the elongated yolk and at the posterior limit of the swim bladder  dissociation and sorting using a BD FACS AriaIII cell sorter. Progenies of photoconverted cells comprise progenies of single EHT photoconversion either EHT pol+ or EHT pol  or whole hemogenic endothelium photoconversion. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019.,,pubmed:40501392,,5 dpf hematopoietic zebrafish cells  session 2,GSM9052756,,tissue:sorted hematopoietic cells|cell type:sorted hematopoietic cells|geo loc name:missing|collection date:missing,5 dpf hematopoietic zebrafish cells  session 2,Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019 Assembly: zebrafish genome Lawson lab version 4.3.2. Supplementary files format and content: Tab separated value files,sorted hematopoietic cells,,Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al.  2018; Manoli and Driever  2012; Samsa et al.  2016. All steps were performed with cooled solutions 4°C  and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly  5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine  at a final concentration of 640 µg/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4°C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies  Cat#: 12605 010 for 10 min on ice  with gentle pipetting every 3 mins  first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g  before the TrypLE was removed and the cells were resuspended in 500 µl FACSmax medium Genlantis  Cat#: T200100. Ultimately  samples were passed through a 40 μm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 µl of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples  gating was done on SSC A vs. FSC A to collect cells  then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher  Cat#: D15106. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019. Briefly  a first step of reverse transcription RT SuperScript III  Thermo Fisher  Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT  primers were removed with an exonuclease ExoI NEB  Cat#: M0293L  and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit  NEB  Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit  NEB  Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher  Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher  Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase  Agilent  Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix  Roche Diagnostics  Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and ß actin  DNA quality control using a TapeStation  Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.,,cell type:sorted hematopoietic cells,GSM9052756,GSM9052756: 5 dpf hematopoietic zebrafish cells  session 2; Danio rerio; RNA Seq,GSM9052756 r1,GSM9052756,1,Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al.  2018; Manoli and Driever  2012; Samsa et al.  2016. All steps were performed with cooled solutions 4°C  and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly  5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine  at a final concentration of 640 µg/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4°C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies  Cat#: 12605 010 for 10 min on ice  with gentle pipetting every 3 mins  first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g  before the TrypLE was removed and the cells were resuspended in 500 µl FACSmax medium Genlantis  Cat#: T200100. Ultimately  samples were passed through a 40 μm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 µl of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples  gating was done on SSC A vs. FSC A to collect cells  then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher  Cat#: D15106. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019. Briefly  a first step of reverse transcription RT SuperScript III  Thermo Fisher  Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT  primers were removed with an exonuclease ExoI NEB  Cat#: M0293L  and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit  NEB  Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit  NEB  Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher  Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher  Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase  Agilent  Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix  Roche Diagnostics  Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and ß actin  DNA quality control using a TapeStation  Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP592701,,,TORCQ_2023_S0_L002_R1_001.fastq.gz TORCQ_2023_S0_L002_R2_001.fastq.gz,fastq fastq,9249291128.0,120120664.0,GSM9052756 r2,0:57 1:20,A:2023532922;C:1427491871;G:1568162363;T:1827659977;N:2402443995,57,20,,,2023532922,1427491871,1568162363,1827659977,2402443995,SRX29213468,SRS25409913,SRA2151098,Institut Pasteur,Institut Pasteur,,,,,,,,,,,,,,,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,marsseq,,France,2025-06-17,Larval,Larval,Blood,Hematopoietic System
36251,SRR34017909,SRX29213468,SRS25409913,SRP592701,PRJNA1278741,Single cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches [scRNA Seq],GSE300039,Transcriptome Analysis,Hematopoietic stem cells HSCs and more committed progenitors collectively referred to as HSPCs emerge from vessels during development  via Endothelial to Hematopoietic Transition EHT. Recently  using the zebrafish embryo  we showed that two EHT cell types emerge from the dorsal aorta  raising the question of their subsequent fate. To address this issue  we established a complex pipeline based on single cell photoconversion and transgenic lines to characterize the abilities of EHT cell progenies to conquer hematopoietic organs and to obtain their transcriptomic profiles. We show that the two EHT cell types lead to partly differentially fated cells  with significant differences in thymus colonization and T lymphoid lineage commitment. In addition  we investigated implantation of HSPCs in niches  with the support of HSPC signatures gata2b and cd34/podocalyxin  retrieved from our single cell datasets. This revealed  at unprecedented resolution  the homing of HSPCs in niches of entire early larvae  including the pronephros  the sub aortic and caudal regions  as well as the area contacting the supra intestinal artery. Our work provides new insights on fundamental aspects of HSPC fate acquisition  from their emergence to their homing in specific niches. Overall design: Single cell transcriptomics analysis of newly born hematopoietic stem and progenitor cells. This dataset comprises progenies of cells photoconverted at 2dpf and sorted by FACS at 5dpf  using the Tgkdrl:nls kikume transgenic line  as well as sorted FACS hematopoietic cells from transgenic reporter lines  namely from the Tgrunx1+23:eGFP and the outcross of the Tgcd41:eGFP and Tggata2b:RFP lines. Larvae were collected post dissection separating the rostral  anterior and posterior region along a transversal section at the posterior limit of the elongated yolk and at the posterior limit of the swim bladder  dissociation and sorting using a BD FACS AriaIII cell sorter. Progenies of photoconverted cells comprise progenies of single EHT photoconversion either EHT pol+ or EHT pol  or whole hemogenic endothelium photoconversion. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019.,,pubmed:40501392,,5 dpf hematopoietic zebrafish cells  session 2,GSM9052756,,tissue:sorted hematopoietic cells|cell type:sorted hematopoietic cells|geo loc name:missing|collection date:missing,5 dpf hematopoietic zebrafish cells  session 2,Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019 Assembly: zebrafish genome Lawson lab version 4.3.2. Supplementary files format and content: Tab separated value files,sorted hematopoietic cells,,Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al.  2018; Manoli and Driever  2012; Samsa et al.  2016. All steps were performed with cooled solutions 4°C  and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly  5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine  at a final concentration of 640 µg/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4°C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies  Cat#: 12605 010 for 10 min on ice  with gentle pipetting every 3 mins  first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g  before the TrypLE was removed and the cells were resuspended in 500 µl FACSmax medium Genlantis  Cat#: T200100. Ultimately  samples were passed through a 40 μm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 µl of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples  gating was done on SSC A vs. FSC A to collect cells  then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher  Cat#: D15106. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019. Briefly  a first step of reverse transcription RT SuperScript III  Thermo Fisher  Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT  primers were removed with an exonuclease ExoI NEB  Cat#: M0293L  and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit  NEB  Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit  NEB  Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher  Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher  Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase  Agilent  Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix  Roche Diagnostics  Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and ß actin  DNA quality control using a TapeStation  Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.,,cell type:sorted hematopoietic cells,GSM9052756,GSM9052756: 5 dpf hematopoietic zebrafish cells  session 2; Danio rerio; RNA Seq,GSM9052756 r1,GSM9052756,1,Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al.  2018; Manoli and Driever  2012; Samsa et al.  2016. All steps were performed with cooled solutions 4°C  and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly  5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine  at a final concentration of 640 µg/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4°C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies  Cat#: 12605 010 for 10 min on ice  with gentle pipetting every 3 mins  first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g  before the TrypLE was removed and the cells were resuspended in 500 µl FACSmax medium Genlantis  Cat#: T200100. Ultimately  samples were passed through a 40 μm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 µl of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples  gating was done on SSC A vs. FSC A to collect cells  then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher  Cat#: D15106. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019. Briefly  a first step of reverse transcription RT SuperScript III  Thermo Fisher  Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT  primers were removed with an exonuclease ExoI NEB  Cat#: M0293L  and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit  NEB  Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit  NEB  Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher  Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher  Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase  Agilent  Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix  Roche Diagnostics  Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and ß actin  DNA quality control using a TapeStation  Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP592701,,,TORCQ_2023_S0_L003_R1_001.fastq.gz TORCQ_2023_S0_L003_R2_001.fastq.gz,fastq fastq,9438695574.0,122580462.0,GSM9052756 r3,0:57 1:20,A:2061159862;C:1455510691;G:1599304279;T:1871072315;N:2451648427,57,20,,,2061159862,1455510691,1599304279,1871072315,2451648427,SRX29213468,SRS25409913,SRA2151098,Institut Pasteur,Institut Pasteur,,,,,,,,,,,,,,,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,marsseq,,France,2025-06-17,Larval,Larval,Blood,Hematopoietic System
36252,SRR34017910,SRX29213468,SRS25409913,SRP592701,PRJNA1278741,Single cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches [scRNA Seq],GSE300039,Transcriptome Analysis,Hematopoietic stem cells HSCs and more committed progenitors collectively referred to as HSPCs emerge from vessels during development  via Endothelial to Hematopoietic Transition EHT. Recently  using the zebrafish embryo  we showed that two EHT cell types emerge from the dorsal aorta  raising the question of their subsequent fate. To address this issue  we established a complex pipeline based on single cell photoconversion and transgenic lines to characterize the abilities of EHT cell progenies to conquer hematopoietic organs and to obtain their transcriptomic profiles. We show that the two EHT cell types lead to partly differentially fated cells  with significant differences in thymus colonization and T lymphoid lineage commitment. In addition  we investigated implantation of HSPCs in niches  with the support of HSPC signatures gata2b and cd34/podocalyxin  retrieved from our single cell datasets. This revealed  at unprecedented resolution  the homing of HSPCs in niches of entire early larvae  including the pronephros  the sub aortic and caudal regions  as well as the area contacting the supra intestinal artery. Our work provides new insights on fundamental aspects of HSPC fate acquisition  from their emergence to their homing in specific niches. Overall design: Single cell transcriptomics analysis of newly born hematopoietic stem and progenitor cells. This dataset comprises progenies of cells photoconverted at 2dpf and sorted by FACS at 5dpf  using the Tgkdrl:nls kikume transgenic line  as well as sorted FACS hematopoietic cells from transgenic reporter lines  namely from the Tgrunx1+23:eGFP and the outcross of the Tgcd41:eGFP and Tggata2b:RFP lines. Larvae were collected post dissection separating the rostral  anterior and posterior region along a transversal section at the posterior limit of the elongated yolk and at the posterior limit of the swim bladder  dissociation and sorting using a BD FACS AriaIII cell sorter. Progenies of photoconverted cells comprise progenies of single EHT photoconversion either EHT pol+ or EHT pol  or whole hemogenic endothelium photoconversion. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019.,,pubmed:40501392,,5 dpf hematopoietic zebrafish cells  session 2,GSM9052756,,tissue:sorted hematopoietic cells|cell type:sorted hematopoietic cells|geo loc name:missing|collection date:missing,5 dpf hematopoietic zebrafish cells  session 2,Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019 Assembly: zebrafish genome Lawson lab version 4.3.2. Supplementary files format and content: Tab separated value files,sorted hematopoietic cells,,Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al.  2018; Manoli and Driever  2012; Samsa et al.  2016. All steps were performed with cooled solutions 4°C  and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly  5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine  at a final concentration of 640 µg/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4°C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies  Cat#: 12605 010 for 10 min on ice  with gentle pipetting every 3 mins  first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g  before the TrypLE was removed and the cells were resuspended in 500 µl FACSmax medium Genlantis  Cat#: T200100. Ultimately  samples were passed through a 40 μm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 µl of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples  gating was done on SSC A vs. FSC A to collect cells  then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher  Cat#: D15106. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019. Briefly  a first step of reverse transcription RT SuperScript III  Thermo Fisher  Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT  primers were removed with an exonuclease ExoI NEB  Cat#: M0293L  and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit  NEB  Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit  NEB  Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher  Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher  Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase  Agilent  Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix  Roche Diagnostics  Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and ß actin  DNA quality control using a TapeStation  Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.,,cell type:sorted hematopoietic cells,GSM9052756,GSM9052756: 5 dpf hematopoietic zebrafish cells  session 2; Danio rerio; RNA Seq,GSM9052756 r1,GSM9052756,1,Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al.  2018; Manoli and Driever  2012; Samsa et al.  2016. All steps were performed with cooled solutions 4°C  and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly  5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine  at a final concentration of 640 µg/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4°C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies  Cat#: 12605 010 for 10 min on ice  with gentle pipetting every 3 mins  first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g  before the TrypLE was removed and the cells were resuspended in 500 µl FACSmax medium Genlantis  Cat#: T200100. Ultimately  samples were passed through a 40 μm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 µl of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples  gating was done on SSC A vs. FSC A to collect cells  then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher  Cat#: D15106. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019. Briefly  a first step of reverse transcription RT SuperScript III  Thermo Fisher  Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT  primers were removed with an exonuclease ExoI NEB  Cat#: M0293L  and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit  NEB  Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit  NEB  Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher  Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher  Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase  Agilent  Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix  Roche Diagnostics  Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and ß actin  DNA quality control using a TapeStation  Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP592701,,,TORCQ_2023_S0_L004_R1_001.fastq.gz TORCQ_2023_S0_L004_R2_001.fastq.gz,fastq fastq,9409346870.0,122199310.0,GSM9052756 r4,0:57 1:20,A:2048111796;C:1451606983;G:1595602008;T:1870010070;N:2444016013,57,20,,,2048111796,1451606983,1595602008,1870010070,2444016013,SRX29213468,SRS25409913,SRA2151098,Institut Pasteur,Institut Pasteur,,,,,,,,,,,,,,,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,marsseq,,France,2025-06-17,Larval,Larval,Blood,Hematopoietic System
36253,SRR34017905,SRX29213467,SRS25409912,SRP592701,PRJNA1278741,Single cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches [scRNA Seq],GSE300039,Transcriptome Analysis,Hematopoietic stem cells HSCs and more committed progenitors collectively referred to as HSPCs emerge from vessels during development  via Endothelial to Hematopoietic Transition EHT. Recently  using the zebrafish embryo  we showed that two EHT cell types emerge from the dorsal aorta  raising the question of their subsequent fate. To address this issue  we established a complex pipeline based on single cell photoconversion and transgenic lines to characterize the abilities of EHT cell progenies to conquer hematopoietic organs and to obtain their transcriptomic profiles. We show that the two EHT cell types lead to partly differentially fated cells  with significant differences in thymus colonization and T lymphoid lineage commitment. In addition  we investigated implantation of HSPCs in niches  with the support of HSPC signatures gata2b and cd34/podocalyxin  retrieved from our single cell datasets. This revealed  at unprecedented resolution  the homing of HSPCs in niches of entire early larvae  including the pronephros  the sub aortic and caudal regions  as well as the area contacting the supra intestinal artery. Our work provides new insights on fundamental aspects of HSPC fate acquisition  from their emergence to their homing in specific niches. Overall design: Single cell transcriptomics analysis of newly born hematopoietic stem and progenitor cells. This dataset comprises progenies of cells photoconverted at 2dpf and sorted by FACS at 5dpf  using the Tgkdrl:nls kikume transgenic line  as well as sorted FACS hematopoietic cells from transgenic reporter lines  namely from the Tgrunx1+23:eGFP and the outcross of the Tgcd41:eGFP and Tggata2b:RFP lines. Larvae were collected post dissection separating the rostral  anterior and posterior region along a transversal section at the posterior limit of the elongated yolk and at the posterior limit of the swim bladder  dissociation and sorting using a BD FACS AriaIII cell sorter. Progenies of photoconverted cells comprise progenies of single EHT photoconversion either EHT pol+ or EHT pol  or whole hemogenic endothelium photoconversion. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019.,,pubmed:40501392,,5 dpf hematopoietic zebrafish cells  session 1,GSM9052755,,tissue:sorted hematopoietic cells|cell type:sorted hematopoietic cells|geo loc name:missing|collection date:missing,5 dpf hematopoietic zebrafish cells  session 1,Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019 Assembly: zebrafish genome Lawson lab version 4.3.2. Supplementary files format and content: Tab separated value files,sorted hematopoietic cells,,Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al.  2018; Manoli and Driever  2012; Samsa et al.  2016. All steps were performed with cooled solutions 4°C  and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly  5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine  at a final concentration of 640 µg/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4°C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies  Cat#: 12605 010 for 10 min on ice  with gentle pipetting every 3 mins  first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g  before the TrypLE was removed and the cells were resuspended in 500 µl FACSmax medium Genlantis  Cat#: T200100. Ultimately  samples were passed through a 40 μm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 µl of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples  gating was done on SSC A vs. FSC A to collect cells  then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher  Cat#: D15106. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019. Briefly  a first step of reverse transcription RT SuperScript III  Thermo Fisher  Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT  primers were removed with an exonuclease ExoI NEB  Cat#: M0293L  and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit  NEB  Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit  NEB  Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher  Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher  Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase  Agilent  Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix  Roche Diagnostics  Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and ß actin  DNA quality control using a TapeStation  Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.,,cell type:sorted hematopoietic cells,GSM9052755,GSM9052755: 5 dpf hematopoietic zebrafish cells  session 1; Danio rerio; RNA Seq,GSM9052755 r1,GSM9052755,1,Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al.  2018; Manoli and Driever  2012; Samsa et al.  2016. All steps were performed with cooled solutions 4°C  and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly  5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine  at a final concentration of 640 µg/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4°C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies  Cat#: 12605 010 for 10 min on ice  with gentle pipetting every 3 mins  first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g  before the TrypLE was removed and the cells were resuspended in 500 µl FACSmax medium Genlantis  Cat#: T200100. Ultimately  samples were passed through a 40 μm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 µl of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples  gating was done on SSC A vs. FSC A to collect cells  then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher  Cat#: D15106. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019. Briefly  a first step of reverse transcription RT SuperScript III  Thermo Fisher  Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT  primers were removed with an exonuclease ExoI NEB  Cat#: M0293L  and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit  NEB  Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit  NEB  Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher  Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher  Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase  Agilent  Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix  Roche Diagnostics  Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and ß actin  DNA quality control using a TapeStation  Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP592701,,,TORCQ_2021_S0_R1_001.fastq.gz TORCQ_2021_S0_R2_001.fastq.gz,fastq fastq,45817068160.0,602856160.0,GSM9052755 r1,0:56 1:20,A:12324583812;C:8979463244;G:11486707902;T:13012728622;N:13584580,56,20,,,12324583812,8979463244,11486707902,13012728622,13584580,SRX29213467,SRS25409912,SRA2151098,Institut Pasteur,Institut Pasteur,,,,,,,,,,,,B,T,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,marsseq,,France,2025-06-17,Larval,Larval,Blood,Hematopoietic System
36254,SRR34017906,SRX29213467,SRS25409912,SRP592701,PRJNA1278741,Single cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches [scRNA Seq],GSE300039,Transcriptome Analysis,Hematopoietic stem cells HSCs and more committed progenitors collectively referred to as HSPCs emerge from vessels during development  via Endothelial to Hematopoietic Transition EHT. Recently  using the zebrafish embryo  we showed that two EHT cell types emerge from the dorsal aorta  raising the question of their subsequent fate. To address this issue  we established a complex pipeline based on single cell photoconversion and transgenic lines to characterize the abilities of EHT cell progenies to conquer hematopoietic organs and to obtain their transcriptomic profiles. We show that the two EHT cell types lead to partly differentially fated cells  with significant differences in thymus colonization and T lymphoid lineage commitment. In addition  we investigated implantation of HSPCs in niches  with the support of HSPC signatures gata2b and cd34/podocalyxin  retrieved from our single cell datasets. This revealed  at unprecedented resolution  the homing of HSPCs in niches of entire early larvae  including the pronephros  the sub aortic and caudal regions  as well as the area contacting the supra intestinal artery. Our work provides new insights on fundamental aspects of HSPC fate acquisition  from their emergence to their homing in specific niches. Overall design: Single cell transcriptomics analysis of newly born hematopoietic stem and progenitor cells. This dataset comprises progenies of cells photoconverted at 2dpf and sorted by FACS at 5dpf  using the Tgkdrl:nls kikume transgenic line  as well as sorted FACS hematopoietic cells from transgenic reporter lines  namely from the Tgrunx1+23:eGFP and the outcross of the Tgcd41:eGFP and Tggata2b:RFP lines. Larvae were collected post dissection separating the rostral  anterior and posterior region along a transversal section at the posterior limit of the elongated yolk and at the posterior limit of the swim bladder  dissociation and sorting using a BD FACS AriaIII cell sorter. Progenies of photoconverted cells comprise progenies of single EHT photoconversion either EHT pol+ or EHT pol  or whole hemogenic endothelium photoconversion. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019.,,pubmed:40501392,,5 dpf hematopoietic zebrafish cells  session 1,GSM9052755,,tissue:sorted hematopoietic cells|cell type:sorted hematopoietic cells|geo loc name:missing|collection date:missing,5 dpf hematopoietic zebrafish cells  session 1,Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019 Assembly: zebrafish genome Lawson lab version 4.3.2. Supplementary files format and content: Tab separated value files,sorted hematopoietic cells,,Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al.  2018; Manoli and Driever  2012; Samsa et al.  2016. All steps were performed with cooled solutions 4°C  and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly  5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine  at a final concentration of 640 µg/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4°C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies  Cat#: 12605 010 for 10 min on ice  with gentle pipetting every 3 mins  first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g  before the TrypLE was removed and the cells were resuspended in 500 µl FACSmax medium Genlantis  Cat#: T200100. Ultimately  samples were passed through a 40 μm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 µl of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples  gating was done on SSC A vs. FSC A to collect cells  then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher  Cat#: D15106. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019. Briefly  a first step of reverse transcription RT SuperScript III  Thermo Fisher  Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT  primers were removed with an exonuclease ExoI NEB  Cat#: M0293L  and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit  NEB  Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit  NEB  Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher  Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher  Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase  Agilent  Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix  Roche Diagnostics  Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and ß actin  DNA quality control using a TapeStation  Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.,,cell type:sorted hematopoietic cells,GSM9052755,GSM9052755: 5 dpf hematopoietic zebrafish cells  session 1; Danio rerio; RNA Seq,GSM9052755 r1,GSM9052755,1,Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al.  2018; Manoli and Driever  2012; Samsa et al.  2016. All steps were performed with cooled solutions 4°C  and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly  5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine  at a final concentration of 640 µg/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4°C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies  Cat#: 12605 010 for 10 min on ice  with gentle pipetting every 3 mins  first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g  before the TrypLE was removed and the cells were resuspended in 500 µl FACSmax medium Genlantis  Cat#: T200100. Ultimately  samples were passed through a 40 μm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 µl of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples  gating was done on SSC A vs. FSC A to collect cells  then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher  Cat#: D15106. Cells were sorted in 384 wells plates 28 plates  in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al.  2020  v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al.  2019. Briefly  a first step of reverse transcription RT SuperScript III  Thermo Fisher  Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT  primers were removed with an exonuclease ExoI NEB  Cat#: M0293L  and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit  NEB  Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit  NEB  Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher  Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher  Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase  Agilent  Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix  Roche Diagnostics  Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and ß actin  DNA quality control using a TapeStation  Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP592701,,,TORCQ_2021_S0_R1_001_small.fastq.gz TORCQ_2021_S0_R2_001_small.fastq.gz,fastq fastq,190000.0,2500.0,GSM9052755 r2,0:56 1:20,A:50399;C:36081;G:47775;T:53618;N:2127,56,20,,,50399,36081,47775,53618,2127,SRX29213467,SRS25409912,SRA2151098,Institut Pasteur,Institut Pasteur,,,,,,,,,,,,B,T,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,marsseq,,France,2025-06-17,Larval,Larval,Blood,Hematopoietic System
39665,SRR2027911,SRX1029315,SRS937775,SRP058376,PRJNA284108,RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures,GSE68920,Transcriptome Analysis,We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.,,pubmed:31832066,,6dpf mpeg1:mCherryPosMmarinumGFPPos rep3,GSM1686459,,source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,6dpf mpeg1:mCherryPosMmarinumGFPPos rep3,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample,zebra fish larvae,Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich,tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,GSM1686459,GSM1686459: 6dpf mpeg1:mCherryPosMmarinumGFPPos rep3; Danio rerio; RNA Seq,GSM1686459,,1,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,GEO Accession:GSM1686459,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058376,,,ZFG-14-09_06_ATTCCT_L003_R1_001.fastq.gz,fastq,988427889.0,19380939.0,GSM1686459 r1,0:51,A:322268594;C:166925867;G:171531103;T:327506982;N:195343,51,,,,322268594,166925867,171531103,327506982,195343,SRX1029315,SRS937775,SRA268539,GEO,"Institute of Biology, Leiden University",1,0.6999,,0.24019,,0.85358,,0.56832,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Netherlands,2015-05-15,Larval,Larval,Blood,Hematopoietic System
39666,SRR2027910,SRX1029314,SRS937773,SRP058376,PRJNA284108,RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures,GSE68920,Transcriptome Analysis,We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.,,pubmed:31832066,,6dpf mpeg1:mCherryPosMmarinumGFPPos rep2,GSM1686458,,source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,6dpf mpeg1:mCherryPosMmarinumGFPPos rep2,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample,zebra fish larvae,Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich,tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,GSM1686458,GSM1686458: 6dpf mpeg1:mCherryPosMmarinumGFPPos rep2; Danio rerio; RNA Seq,GSM1686458,,1,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,GEO Accession:GSM1686458,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058376,,,ZFG-14-09_05_ACTGAT_L003_R1_001.fastq.gz,fastq,846771207.0,16603357.0,GSM1686458 r1,0:51,A:268435928;C:150903620;G:153931870;T:273331733;N:168056,51,,,,268435928,150903620,153931870,273331733,168056,SRX1029314,SRS937773,SRA268539,GEO,"Institute of Biology, Leiden University",1,0.72025,,0.17943,,0.87937,,0.5683,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Netherlands,2015-05-15,Larval,Larval,Blood,Hematopoietic System
39667,SRR2027909,SRX1029313,SRS937774,SRP058376,PRJNA284108,RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures,GSE68920,Transcriptome Analysis,We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.,,pubmed:31832066,,6dpf mpeg1:mCherryPosMmarinumGFPPos rep1,GSM1686457,,source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,6dpf mpeg1:mCherryPosMmarinumGFPPos rep1,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample,zebra fish larvae,Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich,tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,GSM1686457,GSM1686457: 6dpf mpeg1:mCherryPosMmarinumGFPPos rep1; Danio rerio; RNA Seq,GSM1686457,,1,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,GEO Accession:GSM1686457,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058376,,,ZFG-14-09_04_GAGTGG_L003_R1_001.fastq.gz,fastq,807459642.0,15832542.0,GSM1686457 r1,0:51,A:260516660;C:140425216;G:145411663;T:260942267;N:163836,51,,,,260516660,140425216,145411663,260942267,163836,SRX1029313,SRS937774,SRA268539,GEO,"Institute of Biology, Leiden University",1,0.7097,,0.17187,,0.93304,,0.64092,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Netherlands,2015-05-15,Larval,Larval,Blood,Hematopoietic System
39668,SRR2027908,SRX1029312,SRS937776,SRP058376,PRJNA284108,RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures,GSE68920,Transcriptome Analysis,We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.,,pubmed:31832066,,6dpf mpeg1:mCherryPos MmarinumGFPNeg rep3,GSM1686456,,source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,6dpf mpeg1:mCherryPos MmarinumGFPNeg rep3,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample,zebra fish larvae,Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich,tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,GSM1686456,GSM1686456: 6dpf mpeg1:mCherryPos MmarinumGFPNeg rep3; Danio rerio; RNA Seq,GSM1686456,,1,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,GEO Accession:GSM1686456,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058376,,,ZFG-14-09_03_CGTACG_L003_R1_001.fastq.gz,fastq,1523483526.0,29872226.0,GSM1686456 r1,0:51,A:499019794;C:267493952;G:277264815;T:479405699;N:299266,51,,,,499019794,267493952,277264815,479405699,299266,SRX1029312,SRS937776,SRA268539,GEO,"Institute of Biology, Leiden University",1,0.67328,,0.15117,,0.91179,,0.54858,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Netherlands,2015-05-15,Larval,Larval,Blood,Hematopoietic System
39669,SRR2027907,SRX1029311,SRS937777,SRP058376,PRJNA284108,RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures,GSE68920,Transcriptome Analysis,We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.,,pubmed:31832066,,6dpf mpeg1:mCherryPos MmarinumGFPNeg rep2,GSM1686455,,source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,6dpf mpeg1:mCherryPos MmarinumGFPNeg rep2,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample,zebra fish larvae,Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich,tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,GSM1686455,GSM1686455: 6dpf mpeg1:mCherryPos MmarinumGFPNeg rep2; Danio rerio; RNA Seq,GSM1686455,,1,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,GEO Accession:GSM1686455,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058376,,,ZFG-14-09_02_GTTTCG_L003_R1_001.fastq.gz,fastq,938675094.0,18405394.0,GSM1686455 r1,0:51,A:284384359;C:173449465;G:178039777;T:302612825;N:188668,51,,,,284384359,173449465,178039777,302612825,188668,SRX1029311,SRS937777,SRA268539,GEO,"Institute of Biology, Leiden University",1,0.72884,,0.14723,,0.90767,,0.57414,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Netherlands,2015-05-15,Larval,Larval,Blood,Hematopoietic System
39670,SRR2027906,SRX1029310,SRS937778,SRP058376,PRJNA284108,RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures,GSE68920,Transcriptome Analysis,We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.,,pubmed:31832066,,6dpf mpeg1:mCherryPos MmarinumGFPNeg rep1,GSM1686454,,source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,6dpf mpeg1:mCherryPos MmarinumGFPNeg rep1,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample,zebra fish larvae,Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich,tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,GSM1686454,GSM1686454: 6dpf mpeg1:mCherryPos MmarinumGFPNeg rep1; Danio rerio; RNA Seq,GSM1686454,,1,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,GEO Accession:GSM1686454,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058376,,,ZFG-14-09_01_GTGGCC_L003_R1_001.fastq.gz,fastq,1248324348.0,24476948.0,GSM1686454 r1,0:51,A:391067882;C:223380294;G:229132022;T:404526410;N:217740,51,,,,391067882,223380294,229132022,404526410,217740,SRX1029310,SRS937778,SRA268539,GEO,"Institute of Biology, Leiden University",1,0.70232,,0.14257,,0.92894,,0.59305,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Netherlands,2015-05-15,Larval,Larval,Blood,Hematopoietic System
41032,SRR3581739,SRX1797279,SRS1465200,SRP075626,PRJNA322629,Mycobacterial infection of adult zebrafish,PRJNA322629,Other,RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.,,,,Larval non fluorescent cells post macrophage sorting3,C NF3,,breed:*AB|age:4dpf|dev stage:Larval|sex:not determined|tissue:Whole animal following macrophage depletion via FACS|BioSampleModel:Model organism or animal,,,,,,,,,C NF3,C NF3,C NF3,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP075626,,,C_NF3.fastq.gz,fastq,1745512893.0,34225743.0,C NF3.fastq.gz,0:51,A:470456301;C:396221813;G:401458508;T:477287506;N:88765,51,,,,470456301,396221813,401458508,477287506,88765,SRX1797279,SRS1465200,SRA429046,Duke University|Molecular Genetics &amp; Microbiology,Duke University,1,0.92839,,0.06821,,0.73099,,0.44395,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2016-05-25,Larval,Larval,Blood,Hematopoietic System
41033,SRR3581729,SRX1797278,SRS1465199,SRP075626,PRJNA322629,Mycobacterial infection of adult zebrafish,PRJNA322629,Other,RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.,,,,Larval non fluorescent cells post macrophage sorting2,C NF2,,breed:*AB|age:4dpf|dev stage:Larval|sex:not determined|tissue:Whole animal following macrophage depletion via FACS|BioSampleModel:Model organism or animal,,,,,,,,,C NF2,C NF2,C NF2,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP075626,,,C_NF2.fastq.gz,fastq,2116510506.0,41500206.0,C NF2.fastq.gz,0:51,A:580244434;C:475940957;G:474848964;T:585459729;N:16422,51,,,,580244434,475940957,474848964,585459729,16422,SRX1797278,SRS1465199,SRA429045,Duke University|Molecular Genetics &amp; Microbiology,Duke University,1,0.90388,,0.06926,,0.78963,,0.49501,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-06-24,Larval,Larval,Blood,Hematopoietic System
41034,SRR3581718,SRX1797274,SRS1465196,SRP075626,PRJNA322629,Mycobacterial infection of adult zebrafish,PRJNA322629,Other,RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.,,,,Larval non fluorescent cells post macrophage sorting1,C NF1,,breed:*AB|age:4dpf|dev stage:Larval|sex:not determined|tissue:Whole animal following macrophage depletion via FACS|BioSampleModel:Model organism or animal,,,,,,,,,C NF1,C NF1,C NF1,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP075626,,,C_NF1.fastq.gz,fastq,1492422690.0,29263190.0,C NF1.fastq.gz,0:51,A:421145406;C:327412398;G:328273236;T:415327504;N:264146,51,,,,421145406,327412398,328273236,415327504,264146,SRX1797274,SRS1465196,SRA429041,Duke University|Molecular Genetics &amp; Microbiology,Duke University,1,0.82347,,0.08561,,0.75207,,0.45637,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-06-24,Larval,Larval,Blood,Hematopoietic System
51253,SRR8632333,SRX5431034,SRS4411029,SRP186864,PRJNA524286,The miR 199 CDK2 axis modulates neutrophil migration and systemic inflammation,GSE127174,Transcriptome Analysis,We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 199 in neutrophils Overall design: for miRNA profiles  we compared the miRNA present in zebrafish neutrophils and keratinocytes to the whole embryo. for miR 199 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR199 or vector control,,pubmed:31451657,,miR 199 3,GSM3629728,,source name:neutrophils overexpressing miR199|strain background:AB|gentoype/variation:overexpressing miR199|tissue:neutrophils,miR 199 3,"Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000 for Samples 6 11. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter:  for Samples 1 5:  “  alignEndsType EndToEnd   outFilterMismatchNmax 1   outFilterMultimapScoreRange 0   outFilterMultimapNmax 10   outSAMunmapped Within   outFilterScoreMinOverLread 0   outFilterMatchNminOverLread 0   outFilterMatchNmin 16   alignSJDBoverhangMin 1000”  for Samples 6 11: “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  “ s 1 –Q 10”  for Samples 6 11  "" p  Q 10"". The data was filtered: for Samples 1 5 using read count > 10 in more than 1 of the samples;  for Samples 6 11  using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts",neutrophils overexpressing miR199,transgenic zebrafish lines were used to produce embryos. For miRNA profiling  transgenic lines expressing GFP in either neutrophils or apical keratincyes were used. For miR 199 target discovery  transgenic lines expressing miR 199 or a vector control together with a GFP reporter were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish embryos were grown to 3 dpf in embryonic media,strain background:AB|gentoype/variation:overexpressing miR199|tissue:neutrophils,GSM3629728,GSM3629728: miR 199 3; Danio rerio; RNA Seq,GSM3629728,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM3629728,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP186864,,,199-3_S24_L003_R1_001.fastq.gz 199-3_S24_L003_R2_001.fastq.gz,fastq fastq,4220702408.0,27767779.0,GSM3629728 r1,0:76 1:76,A:1146580683;C:960484877;G:940832942;T:1172384006;N:419900,76,76,,,1146580683,960484877,940832942,1172384006,419900,SRX5431034,SRS4411029,SRA852308,GEO,"Department of Biological Sciences, Purdue University",2,0.89723,0.89774,0.11975,0.12234,0.7751,0.77922,0.44498,0.44774,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,smartseq,,United States,2019-02-26,Larval,Larval,Blood,Hematopoietic System