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
38293,SRR1647684,SRX756919,SRS742121,SRP049663,PRJNA266803,Spring Varaemia of Carp Virus SVCV infection of adult zebrafish,GSE63133,Transcriptome Analysis,During viral infection  a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here  we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection  i.e. 6h and 24h post infection. For 12 zebrafish IRFs  we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues  but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7  which together with DrIRF3  was highly induced by SVCV infection. For type I IFNs  zebrafish has four IFN genes  three of which  IFN1/2/3  particularly IFN 1 and IFN 3  were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately  50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection  and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.,,pubmed:25535281,,24S,GSM1541908,,source name:spleen|tissue:spleen|disease state:24h post SVCV infection,24S,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,spleen,,Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:spleen|disease state:24h post SVCV infection,GSM1541908,GSM1541908: 24S; Danio rerio; RNA Seq,GSM1541908,,1,Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1541908,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP049663,,,24S_ATGTCA_L003_R1.fastq,fastq,1207014756.0,23666956.0,GSM1541908 r1,0:51,A:316359100;C:290453604;G:283305513;T:316815698;N:80841,51,,,,316359100,290453604,283305513,316815698,80841,SRX756919,SRS742121,SRA200717,GEO,"Institute of Hydrobiology, Chinese Academy of Sciences",1,0.91158,,0.09021,,0.70867,,0.46907,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2014-11-10,Undetermined,Adult,Spleen,Hematopoietic System
38294,SRR1647683,SRX756918,SRS742119,SRP049663,PRJNA266803,Spring Varaemia of Carp Virus SVCV infection of adult zebrafish,GSE63133,Transcriptome Analysis,During viral infection  a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here  we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection  i.e. 6h and 24h post infection. For 12 zebrafish IRFs  we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues  but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7  which together with DrIRF3  was highly induced by SVCV infection. For type I IFNs  zebrafish has four IFN genes  three of which  IFN1/2/3  particularly IFN 1 and IFN 3  were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately  50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection  and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.,,pubmed:25535281,,6S,GSM1541907,,source name:spleen|tissue:spleen|disease state:6h post SVCV infection,6S,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,spleen,,Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:spleen|disease state:6h post SVCV infection,GSM1541907,GSM1541907: 6S; Danio rerio; RNA Seq,GSM1541907,,1,Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1541907,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP049663,,,6S_AGTTCC_L003_R1.fastq,fastq,1251006540.0,24529540.0,GSM1541907 r1,0:51,A:323805792;C:303846999;G:297418642;T:325862442;N:72665,51,,,,323805792,303846999,297418642,325862442,72665,SRX756918,SRS742119,SRA200717,GEO,"Institute of Hydrobiology, Chinese Academy of Sciences",1,0.92105,,0.09005,,0.71273,,0.46937,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2014-11-10,Undetermined,Adult,Spleen,Hematopoietic System
38295,SRR1647682,SRX756917,SRS742118,SRP049663,PRJNA266803,Spring Varaemia of Carp Virus SVCV infection of adult zebrafish,GSE63133,Transcriptome Analysis,During viral infection  a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here  we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection  i.e. 6h and 24h post infection. For 12 zebrafish IRFs  we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues  but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7  which together with DrIRF3  was highly induced by SVCV infection. For type I IFNs  zebrafish has four IFN genes  three of which  IFN1/2/3  particularly IFN 1 and IFN 3  were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately  50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection  and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.,,pubmed:25535281,,0S,GSM1541906,,source name:spleen|tissue:spleen|disease state:un infected,0S,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,spleen,,Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:spleen|disease state:un infected,GSM1541906,GSM1541906: 0S; Danio rerio; RNA Seq,GSM1541906,,1,Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1541906,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP049663,,,0S_AGTCAA_L003_R1.fastq,fastq,1155087372.0,22648772.0,GSM1541906 r1,0:51,A:301183546;C:279328135;G:272663981;T:301834798;N:76912,51,,,,301183546,279328135,272663981,301834798,76912,SRX756917,SRS742118,SRA200717,GEO,"Institute of Hydrobiology, Chinese Academy of Sciences",1,0.91841,,0.09679,,0.70546,,0.47624,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2014-11-10,Undetermined,Adult,Spleen,Hematopoietic System
39665,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
47583,SRR6661157,SRX3638253,SRS2904504,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,SplWTPHZ 3,GSM2975201,,source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type,SplWTPHZ 3,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type,GSM2975201,GSM2975201: SplWTPHZ 3; Danio rerio; RNA Seq,GSM2975201,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975201,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,SplWTPHZ_3.fastq.gz,fastq,863137362.0,16924262.0,GSM2975201 r1,0:51,A:243029420;C:186621398;G:190769119;T:242704294;N:13131,51,,,,243029420,186621398,190769119,242704294,13131,SRX3638253,SRS2904504,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.94871,,0.18797,,0.7289,,0.48689,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Spleen,Hematopoietic System
47584,SRR6661156,SRX3638252,SRS2904503,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,SplWTPHZ 2,GSM2975200,,source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type,SplWTPHZ 2,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type,GSM2975200,GSM2975200: SplWTPHZ 2; Danio rerio; RNA Seq,GSM2975200,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975200,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,SplWTPHZ_2.fastq.gz,fastq,748057494.0,14667794.0,GSM2975200 r1,0:51,A:212731080;C:159238564;G:163993235;T:212082953;N:11662,51,,,,212731080,159238564,163993235,212082953,11662,SRX3638252,SRS2904503,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.94641,,0.22364,,0.7264,,0.48998,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Spleen,Hematopoietic System
47585,SRR6661155,SRX3638251,SRS2904502,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,SplWTPHZ 1,GSM2975199,,source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type,SplWTPHZ 1,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type,GSM2975199,GSM2975199: SplWTPHZ 1; Danio rerio; RNA Seq,GSM2975199,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975199,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,SplWTPHZ_1.fastq.gz,fastq,771862917.0,15134567.0,GSM2975199 r1,0:51,A:220317243;C:164032479;G:167543123;T:219958265;N:11807,51,,,,220317243,164032479,167543123,219958265,11807,SRX3638251,SRS2904502,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.94835,,0.1926,,0.71453,,0.48677,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Spleen,Hematopoietic System
47586,SRR6661154,SRX3638250,SRS2904501,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,SplWT 3,GSM2975198,,source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type,SplWT 3,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type,GSM2975198,GSM2975198: SplWT 3; Danio rerio; RNA Seq,GSM2975198,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975198,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,SplWT_3.fastq.gz,fastq,815973888.0,15999488.0,GSM2975198 r1,0:51,A:236186435;C:169473350;G:175246943;T:235055142;N:12018,51,,,,236186435,169473350,175246943,235055142,12018,SRX3638250,SRS2904501,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.94554,,0.25855,,0.71873,,0.54675,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Spleen,Hematopoietic System
47587,SRR6661153,SRX3638249,SRS2904499,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,SplWT 2,GSM2975197,,source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type,SplWT 2,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type,GSM2975197,GSM2975197: SplWT 2; Danio rerio; RNA Seq,GSM2975197,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975197,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,SplWT_2.fastq.gz,fastq,909644262.0,17836162.0,GSM2975197 r1,0:51,A:259661486;C:192636111;G:198048163;T:259284494;N:14008,51,,,,259661486,192636111,198048163,259284494,14008,SRX3638249,SRS2904499,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.94781,,0.22979,,0.69962,,0.49839,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Spleen,Hematopoietic System
47588,SRR6661152,SRX3638248,SRS2904500,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,SplWT 1,GSM2975196,,source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type,SplWT 1,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type,GSM2975196,GSM2975196: SplWT 1; Danio rerio; RNA Seq,GSM2975196,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975196,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,SplWT_1.fastq.gz,fastq,888755274.0,17426574.0,GSM2975196 r1,0:51,A:241072815;C:200347978;G:205733626;T:241587449;N:13406,51,,,,241072815,200347978,205733626,241587449,13406,SRX3638248,SRS2904500,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.95759,,0.1342,,0.72918,,0.52233,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Spleen,Hematopoietic System
47589,SRR6661151,SRX3638247,SRS2904498,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,SplDKOPHZ 3,GSM2975195,,source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,SplDKOPHZ 3,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,GSM2975195,GSM2975195: SplDKOPHZ 3; Danio rerio; RNA Seq,GSM2975195,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975195,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,SplDKOPHZ_3.fastq.gz,fastq,881441160.0,17283160.0,GSM2975195 r1,0:51,A:243254581;C:194198200;G:199055092;T:244919975;N:13312,51,,,,243254581,194198200,199055092,244919975,13312,SRX3638247,SRS2904498,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.90441,,0.14881,,0.71447,,0.51129,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Spleen,Hematopoietic System
47590,SRR6661150,SRX3638246,SRS2904497,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,SplDKOPHZ 2,GSM2975194,,source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,SplDKOPHZ 2,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,GSM2975194,GSM2975194: SplDKOPHZ 2; Danio rerio; RNA Seq,GSM2975194,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975194,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,SplDKOPHZ_2.fastq.gz,fastq,795840414.0,15604714.0,GSM2975194 r1,0:51,A:229921467;C:166126021;G:170186584;T:229594266;N:12076,51,,,,229921467,166126021,170186584,229594266,12076,SRX3638246,SRS2904497,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.88657,,0.23556,,0.7194,,0.51207,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Spleen,Hematopoietic System
47591,SRR6661149,SRX3638245,SRS2904495,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,SplDKOPHZ 1,GSM2975193,,source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,SplDKOPHZ 1,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,GSM2975193,GSM2975193: SplDKOPHZ 1; Danio rerio; RNA Seq,GSM2975193,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975193,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,SplDKOPHZ_1.fastq.gz,fastq,788951436.0,15469636.0,GSM2975193 r1,0:51,A:217408862;C:175236911;G:178930271;T:217363444;N:11948,51,,,,217408862,175236911,178930271,217363444,11948,SRX3638245,SRS2904495,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.90945,,0.10065,,0.72468,,0.48596,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Spleen,Hematopoietic System
47592,SRR6661148,SRX3638244,SRS2904496,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,SplDKO 3,GSM2975192,,source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,SplDKO 3,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,GSM2975192,GSM2975192: SplDKO 3; Danio rerio; RNA Seq,GSM2975192,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975192,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,SplDKO_3.fastq.gz,fastq,732609543.0,14364893.0,GSM2975192 r1,0:51,A:209020386;C:154988652;G:160405898;T:208183578;N:11029,51,,,,209020386,154988652,160405898,208183578,11029,SRX3638244,SRS2904496,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.88228,,0.23609,,0.72529,,0.50392,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Spleen,Hematopoietic System
47593,SRR6661147,SRX3638243,SRS2904493,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,SplDKO 2,GSM2975191,,source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,SplDKO 2,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,GSM2975191,GSM2975191: SplDKO 2; Danio rerio; RNA Seq,GSM2975191,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975191,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,SplDKO_2.fastq.gz,fastq,747985635.0,14666385.0,GSM2975191 r1,0:51,A:209892939;C:160527969;G:165683955;T:211869190;N:11582,51,,,,209892939,160527969,165683955,211869190,11582,SRX3638243,SRS2904493,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.90267,,0.20054,,0.7249,,0.53668,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Spleen,Hematopoietic System
47594,SRR6661146,SRX3638242,SRS2904494,SRP131956,PRJNA432507,Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne,GSE109978,Transcriptome Analysis,RNA seq datasets on adult zebrafish kidneys and spleens  non PHZ phenylhydrazine and PHZ treated  to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü  hrg1 doulble knockout DKO  both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.,,pubmed:30248094,,SplDKO 1,GSM2975190,,source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,SplDKO 1,Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR  version 2.5.2b. We counted number of reads mapped to genes using htseq  version 0.6.1p1. Differential gene expression analysis was performed using DESeq2  version 1.12.3  with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10  31 was used  and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation  we used  Ensembl GRCz10  release 87.,whole animal,Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,Normal zebrafish husbandary,tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO,GSM2975190,GSM2975190: SplDKO 1; Danio rerio; RNA Seq,GSM2975190,,1,TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation,GEO Accession:GSM2975190,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP131956,,,SplDKO_1.fastq.gz,fastq,724574391.0,14207341.0,GSM2975190 r1,0:51,A:207549130;C:151913145;G:156789401;T:208311727;N:10988,51,,,,207549130,151913145,156789401,208311727,10988,SRX3638242,SRS2904494,SRA654641,GEO,"Laboratory of Molecular Biology, NIH/NIDDK",1,0.89742,,0.2275,,0.71547,,0.5072,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2018-02-01,Adult,Adult,Spleen,Hematopoietic System
49748,SRR8040452,SRX4870965,SRS3925946,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32lps5 RNA seq,GSM3427234,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32lps5 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427234,GSM3427234: t32lps5 RNA seq; Danio rerio; RNA Seq,GSM3427234,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427234,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2525095950.0,33667946.0,GSM3427234 r1,0:75 1:0,A:654325529;C:574214700;G:560979222;T:735543925;N:32574,75,0,,,654325529,574214700,560979222,735543925,32574,SRX4870965,SRS3925946,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.94279,,0.11158,,0.7739,,0.56131,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49749,SRR8040451,SRX4870964,SRS3925945,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32lps4 RNA seq,GSM3427233,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32lps4 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427233,GSM3427233: t32lps4 RNA seq; Danio rerio; RNA Seq,GSM3427233,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427233,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2324475900.0,30993012.0,GSM3427233 r1,0:75 1:0,A:593299460;C:533734154;G:526980483;T:670430972;N:30831,75,0,,,593299460,533734154,526980483,670430972,30831,SRX4870964,SRS3925945,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.9455,,0.10812,,0.78046,,0.55958,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49750,SRR8040450,SRX4870962,SRS3925943,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32lps3 RNA seq,GSM3427232,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32lps3 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427232,GSM3427232: t32lps3 RNA seq; Danio rerio; RNA Seq,GSM3427232,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427232,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2390945250.0,31879270.0,GSM3427232 r1,0:75 1:0,A:620617289;C:546536575;G:538087155;T:685671110;N:33121,75,0,,,620617289,546536575,538087155,685671110,33121,SRX4870962,SRS3925943,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.94216,,0.12594,,0.74925,,0.54113,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49751,SRR8040449,SRX4870961,SRS3925942,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32lps2 RNA seq,GSM3427231,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32lps2 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427231,GSM3427231: t32lps2 RNA seq; Danio rerio; RNA Seq,GSM3427231,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427231,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2372211900.0,31629492.0,GSM3427231 r1,0:75 1:0,A:609244327;C:553579722;G:546387461;T:662968297;N:32093,75,0,,,609244327,553579722,546387461,662968297,32093,SRX4870961,SRS3925942,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.91064,,0.09975,,0.7318,,0.52325,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49752,SRR8040448,SRX4870960,SRS3925941,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32lps1 RNA seq,GSM3427230,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32lps1 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427230,GSM3427230: t32lps1 RNA seq; Danio rerio; RNA Seq,GSM3427230,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427230,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2601300000.0,34684000.0,GSM3427230 r1,0:75 1:0,A:696279292;C:582818011;G:571718581;T:750447755;N:36361,75,0,,,696279292,582818011,571718581,750447755,36361,SRX4870960,SRS3925941,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.93957,,0.13624,,0.74641,,0.53521,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49753,SRR8040447,SRX4870959,SRS3925940,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32ct10 RNA seq,GSM3427229,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32ct10 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427229,GSM3427229: t32ct10 RNA seq; Danio rerio; RNA Seq,GSM3427229,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427229,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2206367925.0,29418239.0,GSM3427229 r1,0:75 1:0,A:564695219;C:513292663;G:507293808;T:621057423;N:28812,75,0,,,564695219,513292663,507293808,621057423,28812,SRX4870959,SRS3925940,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.94594,,0.10744,,0.75511,,0.39959,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49754,SRR8040446,SRX4870958,SRS3925939,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32ct8 RNA seq,GSM3427228,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32ct8 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427228,GSM3427228: t32ct8 RNA seq; Danio rerio; RNA Seq,GSM3427228,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427228,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2160654900.0,28808732.0,GSM3427228 r1,0:75 1:0,A:560268124;C:491395956;G:494788088;T:614174312;N:28420,75,0,,,560268124,491395956,494788088,614174312,28420,SRX4870958,SRS3925939,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.91437,,0.1131,,0.74661,,0.54441,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49755,SRR8040445,SRX4870957,SRS3925938,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32ct6 RNA seq,GSM3427227,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32ct6 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427227,GSM3427227: t32ct6 RNA seq; Danio rerio; RNA Seq,GSM3427227,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427227,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2175448725.0,29005983.0,GSM3427227 r1,0:75 1:0,A:588911336;C:487829921;G:471925092;T:626753522;N:28854,75,0,,,588911336,487829921,471925092,626753522,28854,SRX4870957,SRS3925938,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.93789,,0.14514,,0.73839,,0.51589,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49756,SRR8040444,SRX4870956,SRS3925937,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32ct3 RNA seq,GSM3427226,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32ct3 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427226,GSM3427226: t32ct3 RNA seq; Danio rerio; RNA Seq,GSM3427226,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427226,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2350450425.0,31339339.0,GSM3427226 r1,0:75 1:0,A:612558543;C:533417342;G:511898107;T:692543546;N:32887,75,0,,,612558543,533417342,511898107,692543546,32887,SRX4870956,SRS3925937,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.88939,,0.13696,,0.74649,,0.5071,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49757,SRR8040443,SRX4870955,SRS3925936,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t32ct2 RNA seq,GSM3427225,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t32ct2 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427225,GSM3427225: t32ct2 RNA seq; Danio rerio; RNA Seq,GSM3427225,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427225,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2500728150.0,33343042.0,GSM3427225 r1,0:75 1:0,A:663109698;C:565815864;G:564300306;T:707468578;N:33704,75,0,,,663109698,565815864,564300306,707468578,33704,SRX4870955,SRS3925936,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.92821,,0.27272,,0.71969,,0.48781,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49758,SRR8040442,SRX4870954,SRS3925988,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28lps8 RNA seq,GSM3427224,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28lps8 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427224,GSM3427224: t28lps8 RNA seq; Danio rerio; RNA Seq,GSM3427224,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427224,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2342903700.0,31238716.0,GSM3427224 r1,0:75 1:0,A:613986696;C:535703169;G:527411229;T:665771221;N:31385,75,0,,,613986696,535703169,527411229,665771221,31385,SRX4870954,SRS3925988,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.92238,,0.11108,,0.75223,,0.54609,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49759,SRR8040441,SRX4870953,SRS3925935,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28lps4 RNA seq,GSM3427223,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28lps4 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427223,GSM3427223: t28lps4 RNA seq; Danio rerio; RNA Seq,GSM3427223,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427223,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2009201550.0,26789354.0,GSM3427223 r1,0:75 1:0,A:503118595;C:466998217;G:461838042;T:577221133;N:25563,75,0,,,503118595,466998217,461838042,577221133,25563,SRX4870953,SRS3925935,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.85044,,0.10362,,0.78149,,0.59209,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49760,SRR8040440,SRX4870952,SRS3925934,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28lps3 RNA seq,GSM3427222,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28lps3 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427222,GSM3427222: t28lps3 RNA seq; Danio rerio; RNA Seq,GSM3427222,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427222,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2262918375.0,30172245.0,GSM3427222 r1,0:75 1:0,A:557712391;C:559312209;G:525961809;T:619902191;N:29775,75,0,,,557712391,559312209,525961809,619902191,29775,SRX4870952,SRS3925934,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.75792,,0.0861,,0.77977,,0.47016,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49761,SRR8040439,SRX4870951,SRS3925933,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28lps2 RNA seq,GSM3427221,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28lps2 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427221,GSM3427221: t28lps2 RNA seq; Danio rerio; RNA Seq,GSM3427221,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427221,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2362744425.0,31503259.0,GSM3427221 r1,0:75 1:0,A:605359081;C:550864600;G:543725417;T:662762619;N:32708,75,0,,,605359081,550864600,543725417,662762619,32708,SRX4870951,SRS3925933,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.92027,,0.10164,,0.7403,,0.52342,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49762,SRR8040438,SRX4870950,SRS3925932,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28lps1 RNA seq,GSM3427220,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28lps1 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427220,GSM3427220: t28lps1 RNA seq; Danio rerio; RNA Seq,GSM3427220,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427220,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2219433000.0,29592440.0,GSM3427220 r1,0:75 1:0,A:559427934;C:519857518;G:513429485;T:626687457;N:30606,75,0,,,559427934,519857518,513429485,626687457,30606,SRX4870950,SRS3925932,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.89861,,0.09731,,0.76889,,0.4978,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49763,SRR8040437,SRX4870949,SRS3925931,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28ct7 RNA seq,GSM3427219,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28ct7 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427219,GSM3427219: t28ct7 RNA seq; Danio rerio; RNA Seq,GSM3427219,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427219,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2329584075.0,31061121.0,GSM3427219 r1,0:75 1:0,A:624440550;C:517755267;G:499439713;T:687917841;N:30704,75,0,,,624440550,517755267,499439713,687917841,30704,SRX4870949,SRS3925931,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.88755,,0.13982,,0.75739,,0.56552,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49764,SRR8040436,SRX4870948,SRS3925930,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28ct5 RNA seq,GSM3427218,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28ct5 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427218,GSM3427218: t28ct5 RNA seq; Danio rerio; RNA Seq,GSM3427218,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427218,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2116347225.0,28217963.0,GSM3427218 r1,0:75 1:0,A:549735276;C:488049942;G:477129323;T:601405177;N:27507,75,0,,,549735276,488049942,477129323,601405177,27507,SRX4870948,SRS3925930,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.94198,,0.11445,,0.75487,,0.53068,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49765,SRR8040435,SRX4870947,SRS3925929,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28ct3 RNA seq,GSM3427217,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28ct3 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427217,GSM3427217: t28ct3 RNA seq; Danio rerio; RNA Seq,GSM3427217,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427217,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2689388775.0,35858517.0,GSM3427217 r1,0:75 1:0,A:723021338;C:600600385;G:595495733;T:770233672;N:37647,75,0,,,723021338,600600385,595495733,770233672,37647,SRX4870947,SRS3925929,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.9433,,0.12005,,0.75175,,0.52805,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49766,SRR8040434,SRX4870946,SRS3925927,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28ct2 RNA seq,GSM3427216,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28ct2 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427216,GSM3427216: t28ct2 RNA seq; Danio rerio; RNA Seq,GSM3427216,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427216,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2358123450.0,31441646.0,GSM3427216 r1,0:75 1:0,A:608599109;C:548957677;G:537939593;T:662594226;N:32845,75,0,,,608599109,548957677,537939593,662594226,32845,SRX4870946,SRS3925927,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.93343,,0.09904,,0.73701,,0.50221,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49767,SRR8040433,SRX4870945,SRS3925928,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t28ct1 RNA seq,GSM3427215,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t28ct1 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427215,GSM3427215: t28ct1 RNA seq; Danio rerio; RNA Seq,GSM3427215,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427215,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2340413625.0,31205515.0,GSM3427215 r1,0:75 1:0,A:601455783;C:547481954;G:534319560;T:657124045;N:32283,75,0,,,601455783,547481954,534319560,657124045,32283,SRX4870945,SRS3925928,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.91963,,0.11224,,0.7363,,0.52602,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49768,SRR8040432,SRX4870944,SRS3925926,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t24lps8 RNA seq,GSM3427214,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t24lps8 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427214,GSM3427214: t24lps8 RNA seq; Danio rerio; RNA Seq,GSM3427214,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427214,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,1914339900.0,25524532.0,GSM3427214 r1,0:75 1:0,A:512209644;C:432894621;G:420067370;T:549142945;N:25320,75,0,,,512209644,432894621,420067370,549142945,25320,SRX4870944,SRS3925926,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.92034,,0.12782,,0.73777,,0.53097,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49769,SRR8040431,SRX4870943,SRS3925925,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t24lps4 RNA seq,GSM3427213,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t24lps4 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427213,GSM3427213: t24lps4 RNA seq; Danio rerio; RNA Seq,GSM3427213,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427213,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2137202850.0,28496038.0,GSM3427213 r1,0:75 1:0,A:542475947;C:498947754;G:490366774;T:605383850;N:28525,75,0,,,542475947,498947754,490366774,605383850,28525,SRX4870943,SRS3925925,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.91347,,0.09882,,0.75763,,0.46833,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System
49770,SRR8040430,SRX4870942,SRS3925924,SRP165277,PRJNA495917,Embryonic incubation temperature has a long term effect on the immune response of adult zebrafish,GSE121163,Transcriptome Analysis,Zebrafish eggs were collected at 28 °C  and split into three embryonic incubation temperature groups 24 °C  28 °C  32 °C. When larvae reaching first feeding  the incubation temperature of larvae from 24 °C and 32 °C was gradually changed to 28 °C  and all fish were kept at 28 °C for later development until maturity. At 100 dpf  7 replicates from each temperature group were intraperitoneally i.p. injected with 2 µl of 50 mg/ml lipopolysaccharide LPS from Pseudomonas aeruginosa 10  while another 7 replicates were i.p. injected with 2 µl phosphate buffered saline as control. At 12 h post injection  the spleen was dissected  and total RNA was extracted. Five LPS treated replicates and five controls were used for building RNA libraries and sequencing. The differential gene expression analysis were performed between fish from different embryonic incubation temperatures 24 °C vs 28 °C; 32 °C vs 28 °C  and between LPS treatment and control within each temperature group 24 °C LPS vs control; 28 °C LPS vs control; 32 °C LPS vs control. Totally  251 differentially expressed genes DEGs  71 up /180 down regulated were identified in fish from 24 °C embryonic incubation temperature compared to fish kept at constant 28 °C DESeq2  adjusted p value < 0.05  |fold change| > 1.5; and 660 DEGs 385 up /275 down regulated were identified in fish from 32 °C embryonic incubation temperature compared to fish kept at 28 °C. By comparing LPS treated fish to control  567 DEGs 271 up /296 down regulated were identified in fish from embryonic incubation temperature of 24 °C  140 DEGs 80 up /60 down regulated were identified in fish kept at constant 28 °C; and 49 DEGs 11 up /38 down regulated were identified in fish from the 32 °C embryonic incubation temperature group. Overall design: Thirty samples were analyzed  including five LPS treated replicates and five controls from each of three embryonic incubation temperatures 24 °C  28 °C  32 °C.,parent bioproject:PRJNA495914,,,t24lps3 RNA seq,GSM3427212,,tissue:spleen|strain:AB|developmental stage:adult|age:100 dpf,t24lps3 RNA seq,Used bcl2fastq for demultiplexing cutadapt v1.12 for trimming adapters FASTX Toolkit for filtering low quality reads FastQC v0.11.5 for quality control Clean reads were mapped to zebrafish transcriptome GRCz11.92 and genome GRCz11 by STAR version 020201 Read counts were extracted from mapping result of STAR  and merged into one matrix DESeq2 v1.11.1 was used for differential gene expression analysis Genome build: GRCz11 Supplementary files format and content: tab delimited matrix containing read counts of each library,spleen,Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate MS 222; Sigma Aldrich  USA and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 Sigma Aldrich  USA  and kept for 12 h. Then  fish were euthanized by immersing in 300 mg/L MS 222. The spleen was dissected immediately  snap frozen in liquid nitrogen  and stored at  80 °C.,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue Sigma Aldrich  USA until first feeding. One third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C  28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS Special Diets Services  SDS  UK 100  200  300  and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.,strain:AB|developmental stage:adult|age:100 dpf,GSM3427212,GSM3427212: t24lps3 RNA seq; Danio rerio; RNA Seq,GSM3427212,,1,Total RNA was isolated from spleen using the PicoPure RNA Isolation kit ThermoFisher Scientific  USA with some modifications. In brief  spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip  and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min  centrifuged at 3 000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube  mixed thoroughly with 100 μl 70% Ethanol  and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially  and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 Agilent Technologies  USA. Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB  USA. Fifty ng total RNAs from each replicate were purified with OligodT beads  fragmented to 200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs cDNAs were synthesized sequentially. The double stranded cDNAs were repaired ends  ligated with universal adaptors on the five prime end and indexed adaptors on the three prime end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s  1 cycle; 98 °C for 10 s  65 °C for 75 s  14 cycles; 65 °C for 5 min  1 cycle. The amplified mRNA libraries were purified with SPRIselect beads  and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 Agilent Technologies  USA.,GEO Accession:GSM3427212,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP165277,,,,,2514206700.0,33522756.0,GSM3427212 r1,0:75 1:0,A:663829025;C:573707517;G:558298485;T:718336661;N:35012,75,0,,,663829025,573707517,558298485,718336661,35012,SRX4870942,SRS3925924,SRA793499,GEO,"Faculty of Biosciences and Aquaculture, Nord University",1,0.93997,,0.11968,,0.74241,,0.53459,,75,,B,,usable mapping rate,illumina,nextseq,5prime,poly_a,nebnext,bulk,unknown,unknown,,Norway,2018-10-12,Adult,Adult,Spleen,Hematopoietic System