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
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
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
51262,SRR8632323,SRX5431024,SRS4411019,SRP186864,PRJNA524286,The miR 199 CDK2 axis modulates neutrophil migration and systemic inflammation,GSE127174,Transcriptome Analysis,We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 199 in neutrophils Overall design: for miRNA profiles  we compared the miRNA present in zebrafish neutrophils and keratinocytes to the whole embryo. for miR 199 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR199 or vector control,,pubmed:31451657,,lyzC+,GSM3629718,,source name:neutrophils|strain background:AB|gentoype/variation:wild type|tissue:neutrophils,lyzC+,"Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000 for Samples 6 11. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter:  for Samples 1 5:  “  alignEndsType EndToEnd   outFilterMismatchNmax 1   outFilterMultimapScoreRange 0   outFilterMultimapNmax 10   outSAMunmapped Within   outFilterScoreMinOverLread 0   outFilterMatchNminOverLread 0   outFilterMatchNmin 16   alignSJDBoverhangMin 1000”  for Samples 6 11: “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  “ s 1 –Q 10”  for Samples 6 11  "" p  Q 10"". The data was filtered: for Samples 1 5 using read count > 10 in more than 1 of the samples;  for Samples 6 11  using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts",neutrophils,transgenic zebrafish lines were used to produce embryos. For miRNA profiling  transgenic lines expressing GFP in either neutrophils or apical keratincyes were used. For miR 199 target discovery  transgenic lines expressing miR 199 or a vector control together with a GFP reporter were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish embryos were grown to 3 dpf in embryonic media,strain background:AB|gentoype/variation:wild type|tissue:neutrophils,GSM3629718,GSM3629718: lyzC+; Danio rerio; RNA Seq,GSM3629718,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM3629718,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP186864,,,lyzc.fastq.gz,fastq,98774200.0,1975484.0,GSM3629718 r1,0:50,A:18442541;C:23267011;G:29755652;T:27302395;N:6601,50,,,,18442541,23267011,29755652,27302395,6601,SRX5431024,SRS4411019,SRA852308,GEO,"Department of Biological Sciences, Purdue University",1,0.24185,,0.03969,,0.94708,,0.65078,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,smartseq,,United States,2019-02-26,Larval,Larval,Blood,Hematopoietic System
54715,SRR10136115,SRX6864204,SRS5401831,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,24: PBS injected fish3,GSM4083497,,source name:PBS injected fish|tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,24: PBS injected fish3,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PBS injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083497,GSM4083497: 24: PBS injected fish3; Danio rerio; RNA Seq,GSM4083497,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083497,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_24_18845_TGACCA_L001_R1_001.fastq.gz,fastq,175231359.0,3435909.0,GSM4083497 r1,0:51,A:43536404;C:41827219;G:40775397;T:49039258;N:53081,51,,,,43536404,41827219,40775397,49039258,53081,SRX6864204,SRS5401831,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.92557,,0.08034,,0.71354,,0.48221,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54716,SRR10136116,SRX6864204,SRS5401831,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,24: PBS injected fish3,GSM4083497,,source name:PBS injected fish|tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,24: PBS injected fish3,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PBS injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083497,GSM4083497: 24: PBS injected fish3; Danio rerio; RNA Seq,GSM4083497,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083497,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_24_18845_TGACCA_L002_R1_001.fastq.gz,fastq,183497490.0,3597990.0,GSM4083497 r2,0:51,A:45576151;C:43814900;G:42692291;T:51382292;N:31856,51,,,,45576151,43814900,42692291,51382292,31856,SRX6864204,SRS5401831,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.92775,,0.08176,,0.71305,,0.47131,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54717,SRR10136113,SRX6864203,SRS5401830,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,23: PBS injected fish2,GSM4083496,,source name:PBS injected fish|tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,23: PBS injected fish2,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PBS injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083496,GSM4083496: 23: PBS injected fish2; Danio rerio; RNA Seq,GSM4083496,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083496,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_23_18844_CGATGT_L001_R1_001.fastq.gz,fastq,178603683.0,3502033.0,GSM4083496 r1,0:51,A:43615081;C:43303795;G:41835813;T:49795688;N:53306,51,,,,43615081,43303795,41835813,49795688,53306,SRX6864203,SRS5401830,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.9227,,0.06923,,0.72547,,0.45761,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54718,SRR10136114,SRX6864203,SRS5401830,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,23: PBS injected fish2,GSM4083496,,source name:PBS injected fish|tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,23: PBS injected fish2,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PBS injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083496,GSM4083496: 23: PBS injected fish2; Danio rerio; RNA Seq,GSM4083496,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083496,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_23_18844_CGATGT_L002_R1_001.fastq.gz,fastq,186816264.0,3663064.0,GSM4083496 r2,0:51,A:45642596;C:45311565;G:43750888;T:52078681;N:32534,51,,,,45642596,45311565,43750888,52078681,32534,SRX6864203,SRS5401830,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.92517,,0.07013,,0.72561,,0.4586,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54719,SRR10136111,SRX6864202,SRS5401829,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,22: PBS injected fish1,GSM4083495,,source name:PBS injected fish|tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,22: PBS injected fish1,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PBS injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083495,GSM4083495: 22: PBS injected fish1; Danio rerio; RNA Seq,GSM4083495,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083495,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_22_18843_ATTCCT_L001_R1_001.fastq.gz,fastq,338607105.0,6639355.0,GSM4083495 r1,0:51,A:83848769;C:81493095;G:77979951;T:95181006;N:104284,51,,,,83848769,81493095,77979951,95181006,104284,SRX6864202,SRS5401829,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.93231,,0.07583,,0.70784,,0.47906,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54720,SRR10136112,SRX6864202,SRS5401829,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,22: PBS injected fish1,GSM4083495,,source name:PBS injected fish|tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,22: PBS injected fish1,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PBS injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083495,GSM4083495: 22: PBS injected fish1; Danio rerio; RNA Seq,GSM4083495,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083495,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_22_18843_ATTCCT_L002_R1_001.fastq.gz,fastq,351800346.0,6898046.0,GSM4083495 r2,0:51,A:87109106;C:84668841;G:81026500;T:98935234;N:60665,51,,,,87109106,84668841,81026500,98935234,60665,SRX6864202,SRS5401829,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.93354,,0.07513,,0.7049,,0.47898,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54721,SRR10136109,SRX6864201,SRS5401828,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,27: Metastases3,GSM4083494,,source name:PC 3M Pro4 injected fish|tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,27: Metastases3,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PC 3M Pro4 injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083494,GSM4083494: 27: Metastases3; Danio rerio; Homo sapiens; RNA Seq,GSM4083494,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083494,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_27_19265_CAGATC_L001_R1_001.fastq.gz,fastq,331816863.0,6506213.0,GSM4083494 r1,0:51,A:82933253;C:78905859;G:76570035;T:93218124;N:189592,51,,,,82933253,78905859,76570035,93218124,189592,SRX6864201,SRS5401828,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.81726,,0.07727,,0.71928,,0.47447,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54722,SRR10136110,SRX6864201,SRS5401828,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,27: Metastases3,GSM4083494,,source name:PC 3M Pro4 injected fish|tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,27: Metastases3,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PC 3M Pro4 injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083494,GSM4083494: 27: Metastases3; Danio rerio; Homo sapiens; RNA Seq,GSM4083494,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083494,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_27_19265_CAGATC_L002_R1_001.fastq.gz,fastq,345788568.0,6780168.0,GSM4083494 r2,0:51,A:86481669;C:82220901;G:79836085;T:97146784;N:103129,51,,,,86481669,82220901,79836085,97146784,103129,SRX6864201,SRS5401828,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.81844,,0.07678,,0.7189,,0.4755,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54723,SRR10136107,SRX6864200,SRS5401827,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,26: Metastases2,GSM4083493,,source name:PC 3M Pro4 injected fish|tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,26: Metastases2,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PC 3M Pro4 injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083493,GSM4083493: 26: Metastases2; Danio rerio; Homo sapiens; RNA Seq,GSM4083493,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083493,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_26_19264_GCCAAT_L001_R1_001.fastq.gz,fastq,381088575.0,7472325.0,GSM4083493 r1,0:51,A:93834091;C:91635540;G:89019328;T:106380009;N:219607,51,,,,93834091,91635540,89019328,106380009,219607,SRX6864200,SRS5401827,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.79302,,0.0612,,0.72803,,0.47524,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54724,SRR10136108,SRX6864200,SRS5401827,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,26: Metastases2,GSM4083493,,source name:PC 3M Pro4 injected fish|tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,26: Metastases2,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PC 3M Pro4 injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083493,GSM4083493: 26: Metastases2; Danio rerio; Homo sapiens; RNA Seq,GSM4083493,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083493,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_26_19264_GCCAAT_L002_R1_001.fastq.gz,fastq,396777450.0,7779950.0,GSM4083493 r2,0:51,A:97747141;C:95409433;G:92718325;T:110778709;N:123842,51,,,,97747141,95409433,92718325,110778709,123842,SRX6864200,SRS5401827,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.79294,,0.06073,,0.72636,,0.47389,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54725,SRR10136105,SRX6864199,SRS5401826,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,25: Metastases1,GSM4083492,,source name:PC 3M Pro4 injected fish|tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,25: Metastases1,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PC 3M Pro4 injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083492,GSM4083492: 25: Metastases1; Danio rerio; Homo sapiens; RNA Seq,GSM4083492,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083492,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_25_19263_ACAGTG_L001_R1_001.fastq.gz,fastq,335771148.0,6583748.0,GSM4083492 r1,0:51,A:82544663;C:80955820;G:79009084;T:93066010;N:195571,51,,,,82544663,80955820,79009084,93066010,195571,SRX6864199,SRS5401826,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.82172,,0.05893,,0.72088,,0.48241,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54726,SRR10136106,SRX6864199,SRS5401826,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,25: Metastases1,GSM4083492,,source name:PC 3M Pro4 injected fish|tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,25: Metastases1,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PC 3M Pro4 injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083492,GSM4083492: 25: Metastases1; Danio rerio; Homo sapiens; RNA Seq,GSM4083492,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083492,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_25_19263_ACAGTG_L002_R1_001.fastq.gz,fastq,348764061.0,6838511.0,GSM4083492 r2,0:51,A:85790391;C:84069256;G:82076851;T:96714974;N:112589,51,,,,85790391,84069256,82076851,96714974,112589,SRX6864199,SRS5401826,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.82119,,0.06015,,0.72299,,0.47492,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
59146,SRR11700449,SRX8259900,SRS6601868,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2wt rep3,GSM4518498,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,cxcr3.2wt 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 GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,GSM4518498,GSM4518498: cxcr3.2wt rep3; Danio rerio; RNA Seq,GSM4518498,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518498,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,wt3_1.fastq.gz,fastq,173026017.0,3392667.0,GSM4518498 r1,0:51,A:50003437;C:34139662;G:34317418;T:54513188;N:52312,51,,,,50003437,34139662,34317418,54513188,52312,SRX8259900,SRS6601868,SRA1072497,GEO,LSHTM,1,0.80078,,0.22125,,0.78788,,0.53444,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59147,SRR11700450,SRX8259900,SRS6601868,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2wt rep3,GSM4518498,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,cxcr3.2wt 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 GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,GSM4518498,GSM4518498: cxcr3.2wt rep3; Danio rerio; RNA Seq,GSM4518498,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518498,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,wt3_2.fastq.gz,fastq,173719362.0,3406262.0,GSM4518498 r2,0:51,A:50217431;C:34289412;G:34447800;T:54729217;N:35502,51,,,,50217431,34289412,34447800,54729217,35502,SRX8259900,SRS6601868,SRA1072497,GEO,LSHTM,1,0.8033,,0.2226,,0.78498,,0.53485,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59148,SRR11700451,SRX8259900,SRS6601868,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2wt rep3,GSM4518498,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,cxcr3.2wt 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 GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,GSM4518498,GSM4518498: cxcr3.2wt rep3; Danio rerio; RNA Seq,GSM4518498,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518498,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,wt3_3.fastq.gz,fastq,117503031.0,2303981.0,GSM4518498 r3,0:51,A:33926847;C:22984117;G:23302421;T:37279310;N:10336,51,,,,33926847,22984117,23302421,37279310,10336,SRX8259900,SRS6601868,SRA1072497,GEO,LSHTM,1,0.76501,,0.22042,,0.79912,,0.54263,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59149,SRR11700452,SRX8259900,SRS6601868,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2wt rep3,GSM4518498,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,cxcr3.2wt 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 GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,GSM4518498,GSM4518498: cxcr3.2wt rep3; Danio rerio; RNA Seq,GSM4518498,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518498,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,wt3_4.fastq.gz,fastq,114086745.0,2236995.0,GSM4518498 r4,0:51,A:32945373;C:22224999;G:22487321;T:36409257;N:19795,51,,,,32945373,22224999,22487321,36409257,19795,SRX8259900,SRS6601868,SRA1072497,GEO,LSHTM,1,0.74509,,0.21675,,0.80653,,0.54624,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59150,SRR11700447,SRX8259899,SRS6601867,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2mu rep3,GSM4518497,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,cxcr3.2mu 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 GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,GSM4518497,GSM4518497: cxcr3.2mu rep3; Danio rerio; RNA Seq,GSM4518497,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518497,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,mu3_1.fastq.gz,fastq,425713881.0,8347331.0,GSM4518497 r1,0:51,A:122037955;C:83276458;G:83884392;T:136385789;N:129287,51,,,,122037955,83276458,83884392,136385789,129287,SRX8259899,SRS6601867,SRA1072497,GEO,LSHTM,1,0.79761,,0.24807,,0.78031,,0.55233,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59151,SRR11700448,SRX8259899,SRS6601867,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2mu rep3,GSM4518497,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,cxcr3.2mu 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 GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,GSM4518497,GSM4518497: cxcr3.2mu rep3; Danio rerio; RNA Seq,GSM4518497,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518497,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,mu3_2.fastq.gz,fastq,432332151.0,8477101.0,GSM4518497 r2,0:51,A:124004077;C:84578395;G:85238663;T:138421813;N:89203,51,,,,124004077,84578395,85238663,138421813,89203,SRX8259899,SRS6601867,SRA1072497,GEO,LSHTM,1,0.79871,,0.25156,,0.77962,,0.54833,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59152,SRR11700445,SRX8259898,SRS6601866,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2wt rep2,GSM4518496,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,cxcr3.2wt 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 GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,GSM4518496,GSM4518496: cxcr3.2wt rep2; Danio rerio; RNA Seq,GSM4518496,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518496,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,wt2_1.fastq.gz,fastq,338884596.0,6644796.0,GSM4518496 r1,0:51,A:95060797;C:69418429;G:69712092;T:104594793;N:98485,51,,,,95060797,69418429,69712092,104594793,98485,SRX8259898,SRS6601866,SRA1072497,GEO,LSHTM,1,0.82037,,0.19262,,0.78573,,0.50787,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59153,SRR11700446,SRX8259898,SRS6601866,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2wt rep2,GSM4518496,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,cxcr3.2wt 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 GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,GSM4518496,GSM4518496: cxcr3.2wt rep2; Danio rerio; RNA Seq,GSM4518496,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518496,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,wt2_2.fastq.gz,fastq,340274448.0,6672048.0,GSM4518496 r2,0:51,A:95520411;C:69702700;G:69990821;T:104992786;N:67730,51,,,,95520411,69702700,69990821,104992786,67730,SRX8259898,SRS6601866,SRA1072497,GEO,LSHTM,1,0.8231,,0.19334,,0.78644,,0.5196,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59154,SRR11700443,SRX8259897,SRS6601865,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2mu rep2,GSM4518495,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,cxcr3.2mu 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 GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,GSM4518495,GSM4518495: cxcr3.2mu rep2; Danio rerio; RNA Seq,GSM4518495,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518495,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,mu2_1.fastq.gz,fastq,289744005.0,5681255.0,GSM4518495 r1,0:51,A:83941467;C:56685263;G:57155798;T:91875606;N:85871,51,,,,83941467,56685263,57155798,91875606,85871,SRX8259897,SRS6601865,SRA1072497,GEO,LSHTM,1,0.797,,0.19874,,0.77948,,0.54924,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59155,SRR11700444,SRX8259897,SRS6601865,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2mu rep2,GSM4518495,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,cxcr3.2mu 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 GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,GSM4518495,GSM4518495: cxcr3.2mu rep2; Danio rerio; RNA Seq,GSM4518495,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518495,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,mu2_2.fastq.gz,fastq,292004937.0,5725587.0,GSM4518495 r2,0:51,A:84614504;C:57133336;G:57626820;T:92570322;N:59955,51,,,,84614504,57133336,57626820,92570322,59955,SRX8259897,SRS6601865,SRA1072497,GEO,LSHTM,1,0.79923,,0.19835,,0.77855,,0.53966,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59156,SRR11700441,SRX8259896,SRS6601864,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2wt rep1,GSM4518494,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,cxcr3.2wt 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 GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,GSM4518494,GSM4518494: cxcr3.2wt rep1; Danio rerio; RNA Seq,GSM4518494,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518494,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,wt1_1.fastq.gz,fastq,365558718.0,7167818.0,GSM4518494 r1,0:51,A:106749458;C:71670361;G:72075682;T:114952902;N:110315,51,,,,106749458,71670361,72075682,114952902,110315,SRX8259896,SRS6601864,SRA1072497,GEO,LSHTM,1,0.80168,,0.20934,,0.78336,,0.55284,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59157,SRR11700442,SRX8259896,SRS6601864,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2wt rep1,GSM4518494,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,cxcr3.2wt 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 GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,GSM4518494,GSM4518494: cxcr3.2wt rep1; Danio rerio; RNA Seq,GSM4518494,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518494,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,wt1_2.fastq.gz,fastq,369956805.0,7254055.0,GSM4518494 r2,0:51,A:108102133;C:72565792;G:72967269;T:116246235;N:75376,51,,,,108102133,72565792,72967269,116246235,75376,SRX8259896,SRS6601864,SRA1072497,GEO,LSHTM,1,0.80058,,0.21005,,0.78303,,0.54972,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59158,SRR11700439,SRX8259895,SRS6601863,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2mu rep1,GSM4518493,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,cxcr3.2mu 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 GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,GSM4518493,GSM4518493: cxcr3.2mu rep1; Danio rerio; RNA Seq,GSM4518493,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518493,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,mu1_1.fastq.gz,fastq,413105049.0,8100099.0,GSM4518493 r1,0:51,A:117770136;C:83069765;G:83597140;T:128544513;N:123495,51,,,,117770136,83069765,83597140,128544513,123495,SRX8259895,SRS6601863,SRA1072497,GEO,LSHTM,1,0.74703,,0.18405,,0.79072,,0.52251,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59159,SRR11700440,SRX8259895,SRS6601863,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2mu rep1,GSM4518493,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,cxcr3.2mu 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 GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,GSM4518493,GSM4518493: cxcr3.2mu rep1; Danio rerio; RNA Seq,GSM4518493,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518493,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,mu1_2.fastq.gz,fastq,417048216.0,8177416.0,GSM4518493 r2,0:51,A:119015831;C:83862032;G:84384304;T:129702704;N:83345,51,,,,119015831,83862032,84384304,129702704,83345,SRX8259895,SRS6601863,SRA1072497,GEO,LSHTM,1,0.74816,,0.18628,,0.78782,,0.52889,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
68081,SRR17604932,SRX13773745,SRS11653746,SRP354901,PRJNA796794,Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation,GSE193591,Transcriptome Analysis,We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit  we were able to identify translating mRNA transcripts in keratinocytes krt4  neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V  transformed keratinocytes  we identified 56 differentially expressed genes in keratinocytes  53 genes in neutrophils  and no differentially expressed genes found in macrophages  compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types,,pubmed:35250998,,Mpeg Ctrl rep3,GSM5814819,,tissue:macrophage|age:3dpf|batch:3|genotype:wild type|cell type:macrophage|cell type id:CL:0000235,Mpeg Ctrl rep3,Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file,macrophage,Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae  or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte  neutrophil  or macrophage specific expression profiling  respectively. ,Larvae were stored at  80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer’s protocols.,,age:3dpf|batch:3|genotype:wild type|cell type:macrophage|cell type id:CL:0000235,GSM5814819,GSM5814819: Mpeg Ctrl rep3; Danio rerio; RNA Seq,GSM5814819 r1,GSM5814819,1,Larvae were stored at  80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP354901,,,D8_GTCGTA_L007_R1_001.fastq.gz,fastq,2252199.0,22299.0,GSM5814819 r1,0:101 1:0,A:514455;C:544764;G:749718;T:443185;N:77,101,0,,,514455,544764,749718,443185,77,SRX13773745,SRS11653746,SRA1356563,University of Wisconsin-Madison,University of Wisconsin-Madison,1,0.85592,,0.229,,0.98664,,0.73589,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2022-01-13,Larval,Larval,Blood,Hematopoietic System
68082,SRR17604933,SRX13773745,SRS11653746,SRP354901,PRJNA796794,Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation,GSE193591,Transcriptome Analysis,We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit  we were able to identify translating mRNA transcripts in keratinocytes krt4  neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V  transformed keratinocytes  we identified 56 differentially expressed genes in keratinocytes  53 genes in neutrophils  and no differentially expressed genes found in macrophages  compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types,,pubmed:35250998,,Mpeg Ctrl rep3,GSM5814819,,tissue:macrophage|age:3dpf|batch:3|genotype:wild type|cell type:macrophage|cell type id:CL:0000235,Mpeg Ctrl rep3,Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file,macrophage,Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae  or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte  neutrophil  or macrophage specific expression profiling  respectively. ,Larvae were stored at  80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer’s protocols.,,age:3dpf|batch:3|genotype:wild type|cell type:macrophage|cell type id:CL:0000235,GSM5814819,GSM5814819: Mpeg Ctrl rep3; Danio rerio; RNA Seq,GSM5814819 r1,GSM5814819,1,Larvae were stored at  80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP354901,,,D8_GTCGTA_L008_R1_001.fastq.gz,fastq,2296235.0,22735.0,GSM5814819 r2,0:101 1:0,A:522320;C:556731;G:765455;T:451622;N:107,101,0,,,522320,556731,765455,451622,107,SRX13773745,SRS11653746,SRA1356563,University of Wisconsin-Madison,University of Wisconsin-Madison,1,0.84559,,0.22391,,0.98646,,0.69194,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2022-01-13,Larval,Larval,Blood,Hematopoietic System
68083,SRR17604934,SRX13773744,SRS11653745,SRP354901,PRJNA796794,Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation,GSE193591,Transcriptome Analysis,We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit  we were able to identify translating mRNA transcripts in keratinocytes krt4  neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V  transformed keratinocytes  we identified 56 differentially expressed genes in keratinocytes  53 genes in neutrophils  and no differentially expressed genes found in macrophages  compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types,,pubmed:35250998,,Lyz Ctrl rep3,GSM5814818,,tissue:neutrophil|age:3dpf|batch:3|genotype:wild type|cell type:neutrophil|cell type id:CL:0000775,Lyz Ctrl rep3,Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file,neutrophil,Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae  or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte  neutrophil  or macrophage specific expression profiling  respectively. ,Larvae were stored at  80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer’s protocols.,,age:3dpf|batch:3|genotype:wild type|cell type:neutrophil|cell type id:CL:0000775,GSM5814818,GSM5814818: Lyz Ctrl rep3; Danio rerio; RNA Seq,GSM5814818 r1,GSM5814818,1,Larvae were stored at  80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP354901,,,D7_AAGCCT_L007_R1_001.fastq.gz,fastq,1017922036.0,10078436.0,GSM5814818 r1,0:101 1:0,A:211263195;C:255471964;G:356158080;T:194948663;N:80134,101,0,,,211263195,255471964,356158080,194948663,80134,SRX13773744,SRS11653745,SRA1356563,University of Wisconsin-Madison,University of Wisconsin-Madison,1,0.9518,,0.21615,,0.94436,,0.70474,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2022-01-13,Larval,Larval,Blood,Hematopoietic System
68084,SRR17604935,SRX13773744,SRS11653745,SRP354901,PRJNA796794,Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation,GSE193591,Transcriptome Analysis,We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit  we were able to identify translating mRNA transcripts in keratinocytes krt4  neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V  transformed keratinocytes  we identified 56 differentially expressed genes in keratinocytes  53 genes in neutrophils  and no differentially expressed genes found in macrophages  compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types,,pubmed:35250998,,Lyz Ctrl rep3,GSM5814818,,tissue:neutrophil|age:3dpf|batch:3|genotype:wild type|cell type:neutrophil|cell type id:CL:0000775,Lyz Ctrl rep3,Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file,neutrophil,Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae  or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte  neutrophil  or macrophage specific expression profiling  respectively. ,Larvae were stored at  80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer’s protocols.,,age:3dpf|batch:3|genotype:wild type|cell type:neutrophil|cell type id:CL:0000775,GSM5814818,GSM5814818: Lyz Ctrl rep3; Danio rerio; RNA Seq,GSM5814818 r1,GSM5814818,1,Larvae were stored at  80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP354901,,,D7_AAGCCT_L008_R1_001.fastq.gz,fastq,1003984137.0,9940437.0,GSM5814818 r2,0:101 1:0,A:208470451;C:251846847;G:350933835;T:192682137;N:50867,101,0,,,208470451,251846847,350933835,192682137,50867,SRX13773744,SRS11653745,SRA1356563,University of Wisconsin-Madison,University of Wisconsin-Madison,1,0.95157,,0.21527,,0.94397,,0.67255,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2022-01-13,Larval,Larval,Blood,Hematopoietic System
68087,SRR17604938,SRX13773742,SRS11653743,SRP354901,PRJNA796794,Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation,GSE193591,Transcriptome Analysis,We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit  we were able to identify translating mRNA transcripts in keratinocytes krt4  neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V  transformed keratinocytes  we identified 56 differentially expressed genes in keratinocytes  53 genes in neutrophils  and no differentially expressed genes found in macrophages  compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types,,pubmed:35250998,,Mpeg V12 rep3,GSM5814816,,tissue:macrophage|age:3dpf|batch:3|genotype:mutant HRas G12V|cell type:macrophage|cell type id:CL:0000235,Mpeg V12 rep3,Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file,macrophage,Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae  or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte  neutrophil  or macrophage specific expression profiling  respectively. ,Larvae were stored at  80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer’s protocols.,,age:3dpf|batch:3|genotype:mutant HRas G12V|cell type:macrophage|cell type id:CL:0000235,GSM5814816,GSM5814816: Mpeg V12 rep3; Danio rerio; RNA Seq,GSM5814816 r1,GSM5814816,1,Larvae were stored at  80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP354901,,,d11_AGCATG_L007_R1_001.fastq.gz,fastq,1117487634.0,11064234.0,GSM5814816 r1,0:101 1:0,A:258329582;C:267694483;G:367895091;T:223479229;N:89249,101,0,,,258329582,267694483,367895091,223479229,89249,SRX13773742,SRS11653743,SRA1356563,University of Wisconsin-Madison,University of Wisconsin-Madison,1,0.84981,,0.20008,,0.89156,,0.65923,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2022-01-13,Larval,Larval,Blood,Hematopoietic System
68088,SRR17604939,SRX13773742,SRS11653743,SRP354901,PRJNA796794,Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation,GSE193591,Transcriptome Analysis,We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit  we were able to identify translating mRNA transcripts in keratinocytes krt4  neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V  transformed keratinocytes  we identified 56 differentially expressed genes in keratinocytes  53 genes in neutrophils  and no differentially expressed genes found in macrophages  compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types,,pubmed:35250998,,Mpeg V12 rep3,GSM5814816,,tissue:macrophage|age:3dpf|batch:3|genotype:mutant HRas G12V|cell type:macrophage|cell type id:CL:0000235,Mpeg V12 rep3,Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file,macrophage,Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae  or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte  neutrophil  or macrophage specific expression profiling  respectively. ,Larvae were stored at  80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer’s protocols.,,age:3dpf|batch:3|genotype:mutant HRas G12V|cell type:macrophage|cell type id:CL:0000235,GSM5814816,GSM5814816: Mpeg V12 rep3; Danio rerio; RNA Seq,GSM5814816 r1,GSM5814816,1,Larvae were stored at  80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP354901,,,d11_AGCATG_L008_R1_001.fastq.gz,fastq,1103643867.0,10927167.0,GSM5814816 r2,0:101 1:0,A:255221519;C:264284982;G:363032184;T:221051396;N:53786,101,0,,,255221519,264284982,363032184,221051396,53786,SRX13773742,SRS11653743,SRA1356563,University of Wisconsin-Madison,University of Wisconsin-Madison,1,0.85088,,0.19956,,0.89108,,0.67953,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2022-01-13,Larval,Larval,Blood,Hematopoietic System
68089,SRR17604940,SRX13773741,SRS11653742,SRP354901,PRJNA796794,Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation,GSE193591,Transcriptome Analysis,We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit  we were able to identify translating mRNA transcripts in keratinocytes krt4  neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V  transformed keratinocytes  we identified 56 differentially expressed genes in keratinocytes  53 genes in neutrophils  and no differentially expressed genes found in macrophages  compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types,,pubmed:35250998,,Lyz V12 rep3,GSM5814815,,tissue:neutrophil|age:3dpf|batch:3|genotype:mutant HRas G12V|cell type:neutrophil|cell type id:CL:0000775,Lyz V12 rep3,Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file,neutrophil,Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae  or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte  neutrophil  or macrophage specific expression profiling  respectively. ,Larvae were stored at  80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer’s protocols.,,age:3dpf|batch:3|genotype:mutant HRas G12V|cell type:neutrophil|cell type id:CL:0000775,GSM5814815,GSM5814815: Lyz V12 rep3; Danio rerio; RNA Seq,GSM5814815 r1,GSM5814815,1,Larvae were stored at  80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP354901,,,d10_GGAGAA_L007_R1_001.fastq.gz,fastq,960647865.0,9511365.0,GSM5814815 r1,0:101 1:0,A:212806547;C:232511926;G:325161334;T:190091050;N:77008,101,0,,,212806547,232511926,325161334,190091050,77008,SRX13773741,SRS11653742,SRA1356563,University of Wisconsin-Madison,University of Wisconsin-Madison,1,0.87006,,0.21965,,0.90788,,0.64906,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2022-01-13,Larval,Larval,Blood,Hematopoietic System
68090,SRR17604941,SRX13773741,SRS11653742,SRP354901,PRJNA796794,Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation,GSE193591,Transcriptome Analysis,We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit  we were able to identify translating mRNA transcripts in keratinocytes krt4  neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V  transformed keratinocytes  we identified 56 differentially expressed genes in keratinocytes  53 genes in neutrophils  and no differentially expressed genes found in macrophages  compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types,,pubmed:35250998,,Lyz V12 rep3,GSM5814815,,tissue:neutrophil|age:3dpf|batch:3|genotype:mutant HRas G12V|cell type:neutrophil|cell type id:CL:0000775,Lyz V12 rep3,Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file,neutrophil,Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae  or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte  neutrophil  or macrophage specific expression profiling  respectively. ,Larvae were stored at  80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer’s protocols.,,age:3dpf|batch:3|genotype:mutant HRas G12V|cell type:neutrophil|cell type id:CL:0000775,GSM5814815,GSM5814815: Lyz V12 rep3; Danio rerio; RNA Seq,GSM5814815 r1,GSM5814815,1,Larvae were stored at  80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP354901,,,d10_GGAGAA_L008_R1_001.fastq.gz,fastq,948355357.0,9389657.0,GSM5814815 r2,0:101 1:0,A:210159593;C:229409756;G:320709432;T:188030646;N:45930,101,0,,,210159593,229409756,320709432,188030646,45930,SRX13773741,SRS11653742,SRA1356563,University of Wisconsin-Madison,University of Wisconsin-Madison,1,0.87179,,0.22092,,0.91029,,0.65705,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2022-01-13,Larval,Larval,Blood,Hematopoietic System
68092,SRR17604943,SRX13773739,SRS11653740,SRP354901,PRJNA796794,Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation,GSE193591,Transcriptome Analysis,We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit  we were able to identify translating mRNA transcripts in keratinocytes krt4  neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V  transformed keratinocytes  we identified 56 differentially expressed genes in keratinocytes  53 genes in neutrophils  and no differentially expressed genes found in macrophages  compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types,,pubmed:35250998,,Mpeg Ctrl rep2,GSM5814813,,tissue:macrophage|age:3dpf|batch:2|genotype:wild type|cell type:macrophage|cell type id:CL:0000235,Mpeg Ctrl rep2,Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file,macrophage,Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae  or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte  neutrophil  or macrophage specific expression profiling  respectively. ,Larvae were stored at  80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer’s protocols.,,age:3dpf|batch:2|genotype:wild type|cell type:macrophage|cell type id:CL:0000235,GSM5814813,GSM5814813: Mpeg Ctrl rep2; Danio rerio; RNA Seq,GSM5814813 r1,GSM5814813,1,Larvae were stored at  80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP354901,,,C8_GTGCTT_L007_R1_001.fastq.gz,fastq,3633285625.0,35973125.0,GSM5814813 r1,0:101 1:0,A:857463844;C:881761168;G:1168499917;T:725509500;N:51196,101,0,,,857463844,881761168,1168499917,725509500,51196,SRX13773739,SRS11653740,SRA1356563,University of Wisconsin-Madison,University of Wisconsin-Madison,1,0.81381,,0.188,,0.91827,,0.76814,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2022-01-13,Larval,Larval,Blood,Hematopoietic System
68093,SRR17604944,SRX13773738,SRS11653739,SRP354901,PRJNA796794,Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation,GSE193591,Transcriptome Analysis,We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit  we were able to identify translating mRNA transcripts in keratinocytes krt4  neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V  transformed keratinocytes  we identified 56 differentially expressed genes in keratinocytes  53 genes in neutrophils  and no differentially expressed genes found in macrophages  compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types,,pubmed:35250998,,Lyz Ctrl rep2,GSM5814812,,tissue:neutrophil|age:3dpf|batch:2|genotype:wild type|cell type:neutrophil|cell type id:CL:0000775,Lyz Ctrl rep2,Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file,neutrophil,Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae  or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte  neutrophil  or macrophage specific expression profiling  respectively. ,Larvae were stored at  80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer’s protocols.,,age:3dpf|batch:2|genotype:wild type|cell type:neutrophil|cell type id:CL:0000775,GSM5814812,GSM5814812: Lyz Ctrl rep2; Danio rerio; RNA Seq,GSM5814812 r1,GSM5814812,1,Larvae were stored at  80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP354901,,,C7_ACCTCA_L007_R1_001.fastq.gz,fastq,6653789605.0,65879105.0,GSM5814812 r1,0:101 1:0,A:1612535065;C:1544008675;G:1997585571;T:1499564492;N:95802,101,0,,,1612535065,1544008675,1997585571,1499564492,95802,SRX13773738,SRS11653739,SRA1356563,University of Wisconsin-Madison,University of Wisconsin-Madison,1,0.47383,,0.11874,,0.94612,,0.76142,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2022-01-13,Larval,Larval,Blood,Hematopoietic System
68095,SRR17604946,SRX13773736,SRS11653737,SRP354901,PRJNA796794,Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation,GSE193591,Transcriptome Analysis,We report the application of Translating Ribosomal Affinity Purification TRAP seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP tagged ribosomal subunit  we were able to identify translating mRNA transcripts in keratinocytes krt4  neutrophils lyz and macrophages mpeg during early cancer transformation. In our zebrafish model of HRasG12V  transformed keratinocytes  we identified 56 differentially expressed genes in keratinocytes  53 genes in neutrophils  and no differentially expressed genes found in macrophages  compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system. Overall design: Comparison of TRAP seq gene expression data in a HRasG12V transformed keratinocyte Zebrafish model in 3 different cells types,,pubmed:35250998,,Mpeg V12 rep2,GSM5814810,,tissue:macrophage|age:3dpf|batch:2|genotype:mutant HRas G12V|cell type:macrophage|cell type id:CL:0000235,Mpeg V12 rep2,Reads were aligned to the transcriptome using Bowtie v1.1.1 Gene abundances were estimated using RSEM v1.2.20 Genome build: GRCz10 Ensembl 83 annotation Supplementary files format and content: The processed data file for each sample is the gene level abundance output of RSEM and is a tab delimited text file,macrophage,Zebrafish larvae were microinjected into one cell stage embryos and screened 3 dpf for transgene expression. Microinjections for TRAP RNA sequencing included either control pTol2 krt4 RFP HRas or oncogenic pTol2 krt4 RFP HRasG12V constructs injected with pTol2 krt4 GFP L10a in wildtype larvae  or into TgLyzC:EGFP L10a or Tgmpeg1:EGFP L10a larvae for keratinocyte  neutrophil  or macrophage specific expression profiling  respectively. ,Larvae were stored at  80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer’s protocols.,,age:3dpf|batch:2|genotype:mutant HRas G12V|cell type:macrophage|cell type id:CL:0000235,GSM5814810,GSM5814810: Mpeg V12 rep2; Danio rerio; RNA Seq,GSM5814810 r1,GSM5814810,1,Larvae were stored at  80°C in minimal residual media. QIAshredder Quiagen was used to homogenize the larvae prior to immunoprecipitation. mRNA was isolated from immunoprecipitated polysomes from 50 pooled oncogene expressing fish or controls using TRIzol reagent Invitrogen. RNA quality and concentration was assessed on Agilent RNA PicoChip and samples with a concentration < 200 pg/µl were concentrated in a SpeedVac. As RNA concentrations were low  library prep was done with the NuGEN Ovation Single Cell RNA Seq System with 20 cycles of amplification. Libraries were then checked by QuBit and an AATI Fragment Analyzer for concentration and fragment size. Adaptors with barcodes were used and samples were sequenced on an Illumina HiSeq with an average of 8 samples per lane  following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP354901,,,C11_AAGAGG_L007_R1_001.fastq.gz,fastq,2065771281.0,20453181.0,GSM5814810 r1,0:101 1:0,A:507674562;C:495211667;G:618229279;T:444625380;N:30393,101,0,,,507674562,495211667,618229279,444625380,30393,SRX13773736,SRS11653737,SRA1356563,University of Wisconsin-Madison,University of Wisconsin-Madison,1,0.9099,,0.2577,,0.83524,,0.69559,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,United States,2022-01-13,Larval,Larval,Blood,Hematopoietic System