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
42501,SRR5683317,SRX2918465,SRS2284474,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 14 xxx post injury Round2 cryo3,GSM2668116,,source name:Mpeg 14 xxx post injury Round2 cryo3|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,Mpeg 14 xxx post injury Round2 cryo3,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 14 xxx post injury Round2 cryo3,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,GSM2668116,GSM2668116: Mpeg 14 xxx post injury Round2 cryo3; Danio rerio; RNA Seq,GSM2668116,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668116,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,cryo3_14dpi_B_R1.fastq.gz cryo3_14dpi_B_R2.fastq.gz,fastq fastq,7861934638.0,49554149.0,GSM2668116 r1,0:79.32 1:79.33,A:2180198909;C:1707559679;G:1786562980;T:2185442888;N:2170182,79,79,,,2180198909,1707559679,1786562980,2185442888,2170182,SRX2918465,SRS2284474,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.92041,0.92378,0.14221,0.14168,0.79799,0.8016,0.45038,0.35896,80,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42502,SRR5683316,SRX2918464,SRS2284472,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 14 xxx post injury Round2 cryo2,GSM2668115,,source name:Mpeg 14 xxx post injury Round2 cryo2|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,Mpeg 14 xxx post injury Round2 cryo2,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 14 xxx post injury Round2 cryo2,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,GSM2668115,GSM2668115: Mpeg 14 xxx post injury Round2 cryo2; Danio rerio; RNA Seq,GSM2668115,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668115,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,cryo2_14dpi_B_R1.fastq.gz cryo2_14dpi_B_R2.fastq.gz,fastq fastq,8095516200.0,51058824.0,GSM2668115 r1,0:79.28 1:79.28,A:2251179258;C:1721305507;G:1814673340;T:2305885309;N:2472786,79,79,,,2251179258,1721305507,1814673340,2305885309,2472786,SRX2918464,SRS2284472,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.89889,0.89756,0.18338,0.17899,0.81219,0.81525,0.43098,0.4397,80,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42503,SRR5683314,SRX2918463,SRS2284471,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 14 xxx post injury Round2 cryo1 merged,GSM2668114,,source name:Mpeg 14 xxx post injury Round2 cryo1 merged|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,Mpeg 14 xxx post injury Round2 cryo1 merged,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 14 xxx post injury Round2 cryo1 merged,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,GSM2668114,GSM2668114: Mpeg 14 xxx post injury Round2 cryo1 merged; Danio rerio; RNA Seq,GSM2668114,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668114,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,14dpicryo1_mpeg_B_R1_May.fastq.gz 14dpicryo1_mpeg_B_R2_May.fastq.gz,fastq fastq,3423280266.0,21561025.0,GSM2668114 r1,0:79.38 1:79.39,A:1107875201;C:594804208;G:621478979;T:1098524417;N:597461,79,79,,,1107875201,594804208,621478979,1098524417,597461,SRX2918463,SRS2284471,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.82792,0.82592,0.70435,0.70409,0.7963,0.81209,0.49674,0.50012,80,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42504,SRR5683315,SRX2918463,SRS2284471,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 14 xxx post injury Round2 cryo1 merged,GSM2668114,,source name:Mpeg 14 xxx post injury Round2 cryo1 merged|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,Mpeg 14 xxx post injury Round2 cryo1 merged,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 14 xxx post injury Round2 cryo1 merged,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,GSM2668114,GSM2668114: Mpeg 14 xxx post injury Round2 cryo1 merged; Danio rerio; RNA Seq,GSM2668114,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668114,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,14dpicryo1_mpeg_B_R1_June.fastq.gz 14dpicryo1_mpeg_B_R2_June.fastq.gz,fastq fastq,610753180.0,3844389.0,GSM2668114 r2,0:79.43 1:79.44,A:194990113;C:106753101;G:111444912;T:197419441;N:145613,79,79,,,194990113,106753101,111444912,197419441,145613,SRX2918463,SRS2284471,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.83295,0.83136,0.71203,0.71039,0.79902,0.80957,0.50147,0.50457,80,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42505,SRR5683313,SRX2918462,SRS2284470,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 14 xxx post injury Round2 sham3,GSM2668113,,source name:Mpeg 14 xxx post injury Round2 sham3|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,Mpeg 14 xxx post injury Round2 sham3,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 14 xxx post injury Round2 sham3,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,GSM2668113,GSM2668113: Mpeg 14 xxx post injury Round2 sham3; Danio rerio; RNA Seq,GSM2668113,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668113,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,sham3_14dpi_B_R1.fastq.gz sham3_14dpi_B_R2.fastq.gz,fastq fastq,6045529728.0,38096625.0,GSM2668113 r1,0:79.34 1:79.35,A:1692396398;C:1295917589;G:1361588402;T:1694052830;N:1574509,79,79,,,1692396398,1295917589,1361588402,1694052830,1574509,SRX2918462,SRS2284470,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.91926,0.91739,0.11828,0.11628,0.82223,0.82534,0.47847,0.49838,80,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42506,SRR5683309,SRX2918461,SRS2284469,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 14 xxx post injury Round1 sham3 merged,GSM2668112,,source name:Mpeg 14 xxx post injury Round1 sham3 merged|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,Mpeg 14 xxx post injury Round1 sham3 merged,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 14 xxx post injury Round1 sham3 merged,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,GSM2668112,GSM2668112: Mpeg 14 xxx post injury Round1 sham3 merged; Danio rerio; RNA Seq,GSM2668112,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668112,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,14dpisham3_mpeg_B_R1_May.fastq.gz 14dpisham3_mpeg_B_R2_May.fastq.gz,fastq fastq,3088232153.0,19713193.0,GSM2668112 r1,0:78.31 1:78.34,A:921823592;C:606907388;G:646058581;T:910627373;N:2815219,78,78,,,921823592,606907388,646058581,910627373,2815219,SRX2918461,SRS2284469,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.87257,0.87547,0.20876,0.20608,0.81253,0.81773,0.44997,0.46461,80,79,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42507,SRR5683311,SRX2918461,SRS2284469,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 14 xxx post injury Round1 sham3 merged,GSM2668112,,source name:Mpeg 14 xxx post injury Round1 sham3 merged|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,Mpeg 14 xxx post injury Round1 sham3 merged,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 14 xxx post injury Round1 sham3 merged,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,GSM2668112,GSM2668112: Mpeg 14 xxx post injury Round1 sham3 merged; Danio rerio; RNA Seq,GSM2668112,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668112,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,14dpisham3_mpeg_B_R1_June.fastq.gz 14dpisham3_mpeg_B_R2_June.fastq.gz,fastq fastq,846302505.0,5389309.0,GSM2668112 r2,0:78.51 1:78.53,A:245478169;C:167755451;G:179179261;T:253210722;N:678902,78,78,,,245478169,167755451,179179261,253210722,678902,SRX2918461,SRS2284469,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.87646,0.87747,0.20632,0.20462,0.81272,0.81897,0.46568,0.46082,78,79,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42508,SRR5683308,SRX2918460,SRS2284468,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 14 xxx post injury Round1 sham2,GSM2668111,,source name:Mpeg 14 xxx post injury Round1 sham2|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,Mpeg 14 xxx post injury Round1 sham2,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 14 xxx post injury Round1 sham2,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,GSM2668111,GSM2668111: Mpeg 14 xxx post injury Round1 sham2; Danio rerio; RNA Seq,GSM2668111,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668111,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,14dpisham2_mpeg_B_R1.fastq.gz 14dpisham2_mpeg_B_R2.fastq.gz,fastq fastq,6035307225.0,38834475.0,GSM2668111 r1,0:77.69 1:77.73,A:1766010265;C:1217065541;G:1295674905;T:1748007248;N:8549266,77,77,,,1766010265,1217065541,1295674905,1748007248,8549266,SRX2918460,SRS2284468,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.87025,0.87255,0.16504,0.16092,0.82075,0.8252,0.48031,0.38246,80,79,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42509,SRR5683307,SRX2918459,SRS2284467,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 14 xxx post injury Round1 sham1,GSM2668110,,source name:Mpeg 14 xxx post injury Round1 sham1|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,Mpeg 14 xxx post injury Round1 sham1,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 14 xxx post injury Round1 sham1,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,GSM2668110,GSM2668110: Mpeg 14 xxx post injury Round1 sham1; Danio rerio; RNA Seq,GSM2668110,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668110,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,14dpisham1_mpeg_B_R1.fastq.gz 14dpisham1_mpeg_B_R2.fastq.gz,fastq fastq,12977926933.0,85345256.0,GSM2668110 r1,0:76.00 1:76.06,A:3815859192;C:2608097642;G:2746153398;T:3772773322;N:35043379,76,76,,,3815859192,2608097642,2746153398,3772773322,35043379,SRX2918459,SRS2284467,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.84194,0.84592,0.19588,0.19184,0.82022,0.82373,0.49431,0.48674,80,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42510,SRR5683306,SRX2918458,SRS2284466,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 5 xxx post injury resec2,GSM2668109,,source name:Mpeg 5 xxx post injury resec2|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse,Mpeg 5 xxx post injury resec2,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 5 xxx post injury resec2,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse,GSM2668109,GSM2668109: Mpeg 5 xxx post injury resec2; Danio rerio; RNA Seq,GSM2668109,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668109,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,mpeg_5dpi_resec2_R1.fastq.gz mpeg_5dpi_resec2_R2.fastq.gz,fastq fastq,3383380650.0,21264204.0,GSM2668109 r1,0:79.56 1:79.56,A:1033165656;C:667727603;G:708080342;T:973980006;N:427043,79,79,,,1033165656,667727603,708080342,973980006,427043,SRX2918458,SRS2284466,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.86066,0.85477,0.25065,0.25874,0.8072,0.81586,0.45299,0.45757,80,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42511,SRR5683305,SRX2918457,SRS2284465,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 5 xxx post injury resec1,GSM2668108,,source name:Mpeg 5 xxx post injury resec1|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse,Mpeg 5 xxx post injury resec1,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 5 xxx post injury resec1,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse,GSM2668108,GSM2668108: Mpeg 5 xxx post injury resec1; Danio rerio; RNA Seq,GSM2668108,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668108,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,mpeg_5dpi_resec1_R1.fastq.gz mpeg_5dpi_resec1_R2.fastq.gz,fastq fastq,6869873301.0,43173364.0,GSM2668108 r1,0:79.56 1:79.56,A:2031090336;C:1426974358;G:1499082453;T:1911947654;N:778500,79,79,,,2031090336,1426974358,1499082453,1911947654,778500,SRX2918457,SRS2284465,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.89183,0.88662,0.13918,0.13872,0.81284,0.81736,0.39007,0.49219,78,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42512,SRR5683304,SRX2918456,SRS2284463,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 5 xxx post injury cryo4,GSM2668107,,source name:Mpeg 5 xxx post injury cryo4|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,Mpeg 5 xxx post injury cryo4,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 5 xxx post injury cryo4,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,GSM2668107,GSM2668107: Mpeg 5 xxx post injury cryo4; Danio rerio; RNA Seq,GSM2668107,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668107,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,mpeg_5dpi_cryo4_R1.fastq.gz mpeg_5dpi_cryo4_R2.fastq.gz,fastq fastq,6277247450.0,39463081.0,GSM2668107 r1,0:79.53 1:79.54,A:1929673813;C:1267115857;G:1307899881;T:1772085832;N:472067,79,79,,,1929673813,1267115857,1307899881,1772085832,472067,SRX2918456,SRS2284463,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.85203,0.8343,0.24868,0.25,0.81308,0.82647,0.48925,0.50311,80,79,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42513,SRR5683303,SRX2918455,SRS2284464,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 5 xxx post injury cryo1,GSM2668106,,source name:Mpeg 5 xxx post injury cryo1|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,Mpeg 5 xxx post injury cryo1,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 5 xxx post injury cryo1,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,GSM2668106,GSM2668106: Mpeg 5 xxx post injury cryo1; Danio rerio; RNA Seq,GSM2668106,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668106,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,mpeg_5dpi_cryo1_R1.fastq.gz mpeg_5dpi_cryo1_R2.fastq.gz,fastq fastq,4027290734.0,25319007.0,GSM2668106 r1,0:79.53 1:79.53,A:1233222560;C:810894366;G:838434971;T:1144395366;N:343471,79,79,,,1233222560,810894366,838434971,1144395366,343471,SRX2918455,SRS2284464,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.85923,0.84321,0.1985,0.20039,0.83625,0.84236,0.49381,0.48397,80,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42514,SRR5683302,SRX2918454,SRS2284462,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 5 xxx post injury sham3,GSM2668105,,source name:Mpeg 5 xxx post injury sham3|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,Mpeg 5 xxx post injury sham3,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 5 xxx post injury sham3,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,GSM2668105,GSM2668105: Mpeg 5 xxx post injury sham3; Danio rerio; RNA Seq,GSM2668105,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668105,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,mpeg_5dpi_sham3_R2.fastq.gz mpeg_5dpi_sham3_R1.fastq.gz,fastq fastq,8115490925.0,51002382.0,GSM2668105 r1,0:79.56 1:79.56,A:2440332785;C:1628963788;G:1720872185;T:2324279946;N:1042221,79,79,,,2440332785,1628963788,1720872185,2324279946,1042221,SRX2918454,SRS2284462,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.85247,0.84621,0.27035,0.27069,0.85084,0.85451,0.45753,0.45612,80,79,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42515,SRR5683300,SRX2918453,SRS2284461,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 5 xxx post injury sham2 merged,GSM2668104,,source name:Mpeg 5 xxx post injury sham2 merged|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,Mpeg 5 xxx post injury sham2 merged,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 5 xxx post injury sham2 merged,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,GSM2668104,GSM2668104: Mpeg 5 xxx post injury sham2 merged; Danio rerio; RNA Seq,GSM2668104,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668104,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,5dpisham2_mpeg_A_R2_April.fastq.gz 5dpisham2_mpeg_A_R1_April.fastq.gz,fastq fastq,3860992328.0,24366329.0,GSM2668104 r1,0:79.22 1:79.23,A:1130628484;C:798981479;G:837808724;T:1092372622;N:1201019,79,79,,,1130628484,798981479,837808724,1092372622,1201019,SRX2918453,SRS2284461,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.89802,0.89614,0.23222,0.22961,0.79894,0.8056,0.40655,0.416,80,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42516,SRR5683301,SRX2918453,SRS2284461,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 5 xxx post injury sham2 merged,GSM2668104,,source name:Mpeg 5 xxx post injury sham2 merged|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,Mpeg 5 xxx post injury sham2 merged,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 5 xxx post injury sham2 merged,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,GSM2668104,GSM2668104: Mpeg 5 xxx post injury sham2 merged; Danio rerio; RNA Seq,GSM2668104,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668104,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,5dpisham2_mpeg_A_R2_June.fastq.gz 5dpisham2_mpeg_A_R1_June.fastq.gz,fastq fastq,1457479078.0,9196316.0,GSM2668104 r2,0:79.24 1:79.24,A:416316844;C:300713902;G:316902348;T:423075764;N:470220,79,79,,,416316844,300713902,316902348,423075764,470220,SRX2918453,SRS2284461,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.89427,0.89319,0.2414,0.23951,0.80259,0.80842,0.40686,0.41528,80,78,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42517,SRR5683299,SRX2918452,SRS2284460,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 1 xxx post injury resec4,GSM2668103,,source name:Mpeg 1 xxx post injury resec4|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse,Mpeg 1 xxx post injury resec4,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 1 xxx post injury resec4,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse,GSM2668103,GSM2668103: Mpeg 1 xxx post injury resec4; Danio rerio; RNA Seq,GSM2668103,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668103,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,mpeg_1dpi_resec4_R1.fastq.gz mpeg_1dpi_resec4_R2.fastq.gz,fastq fastq,5609751993.0,35249823.0,GSM2668103 r1,0:79.57 1:79.57,A:1726370842;C:1096706423;G:1151202056;T:1634668514;N:804158,79,79,,,1726370842,1096706423,1151202056,1634668514,804158,SRX2918452,SRS2284460,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.85046,0.84548,0.24214,0.24515,0.77538,0.78123,0.4936,0.48972,80,79,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42518,SRR5683298,SRX2918451,SRS2284459,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg xxx post injury resec3,GSM2668102,,source name:Mpeg xxx post injury resec3|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse,Mpeg xxx post injury resec3,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg xxx post injury resec3,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse,GSM2668102,GSM2668102: Mpeg xxx post injury resec3; Danio rerio; RNA Seq,GSM2668102,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668102,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,mpeg_1dpi_resec3_R2.fastq.gz mpeg_1dpi_resec3_R1.fastq.gz,fastq fastq,5982719209.0,37588800.0,GSM2668102 r1,0:79.58 1:79.58,A:1830395391;C:1164413802;G:1227508893;T:1759666888;N:734235,79,79,,,1830395391,1164413802,1227508893,1759666888,734235,SRX2918451,SRS2284459,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.84899,0.84538,0.24802,0.24928,0.77352,0.77958,0.48455,0.48731,80,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42519,SRR5683297,SRX2918450,SRS2284458,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg xxx post injury resec2,GSM2668101,,source name:Mpeg xxx post injury resec2|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse,Mpeg xxx post injury resec2,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg xxx post injury resec2,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse,GSM2668101,GSM2668101: Mpeg xxx post injury resec2; Danio rerio; RNA Seq,GSM2668101,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668101,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,mpeg_1dpi_resec2_R2.fastq.gz mpeg_1dpi_resec2_R1.fastq.gz,fastq fastq,5076782892.0,31911484.0,GSM2668101 r1,0:79.54 1:79.55,A:1549105925;C:1013432083;G:1063735890;T:1449731944;N:777050,79,79,,,1549105925,1013432083,1063735890,1449731944,777050,SRX2918450,SRS2284458,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.8623,0.85895,0.22428,0.22646,0.77378,0.78246,0.4794,0.47986,80,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42520,SRR5683296,SRX2918449,SRS2284457,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 1 xxx post injury cryo3,GSM2668100,,source name:Mpeg 1 xxx post injury cryo3|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,Mpeg 1 xxx post injury cryo3,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 1 xxx post injury cryo3,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,GSM2668100,GSM2668100: Mpeg 1 xxx post injury cryo3; Danio rerio; RNA Seq,GSM2668100,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668100,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,mpeg_1dpi_cryo3_R1.fastq.gz mpeg_1dpi_cryo3_R2.fastq.gz,fastq fastq,11880750994.0,75033249.0,GSM2668100 r1,0:79.16 1:79.18,A:3655884756;C:2399881665;G:2467642327;T:3355036709;N:2305537,79,79,,,3655884756,2399881665,2467642327,3355036709,2305537,SRX2918449,SRS2284457,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.88646,0.87912,0.09292,0.08786,0.84867,0.85184,0.60254,0.60389,80,79,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42521,SRR5683295,SRX2918448,SRS2284456,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 1 xxx post injury cryo2,GSM2668099,,source name:Mpeg 1 xxx post injury cryo2|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,Mpeg 1 xxx post injury cryo2,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 1 xxx post injury cryo2,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,GSM2668099,GSM2668099: Mpeg 1 xxx post injury cryo2; Danio rerio; RNA Seq,GSM2668099,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668099,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,mpeg_1dpi_cryo2_R1.fastq.gz mpeg_1dpi_cryo2_R2.fastq.gz,fastq fastq,8232458249.0,51981300.0,GSM2668099 r1,0:79.19 1:79.19,A:2515938515;C:1635124065;G:1691955854;T:2387623909;N:1815906,79,79,,,2515938515,1635124065,1691955854,2387623909,1815906,SRX2918448,SRS2284456,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.84555,0.8442,0.15288,0.14711,0.85123,0.85222,0.49769,0.49241,80,79,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42522,SRR5683294,SRX2918447,SRS2284455,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 1 xxx post injury sham3,GSM2668098,,source name:Mpeg 1 xxx post injury sham3|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,Mpeg 1 xxx post injury sham3,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 1 xxx post injury sham3,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,GSM2668098,GSM2668098: Mpeg 1 xxx post injury sham3; Danio rerio; RNA Seq,GSM2668098,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668098,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,mpeg_1dpi_sham3_R1.fastq.gz mpeg_1dpi_sham3_R2.fastq.gz,fastq fastq,8496331498.0,53397150.0,GSM2668098 r1,0:79.56 1:79.56,A:2502482113;C:1814852881;G:1898533497;T:2279486892;N:976115,79,79,,,2502482113,1814852881,1898533497,2279486892,976115,SRX2918447,SRS2284455,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.91041,0.90731,0.06459,0.06347,0.87945,0.88032,0.49844,0.49408,80,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42523,SRR5683293,SRX2918446,SRS2284453,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 1 xxx post injury sham2,GSM2668097,,source name:Mpeg 1 xxx post injury sham2|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,Mpeg 1 xxx post injury sham2,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 1 xxx post injury sham2,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,GSM2668097,GSM2668097: Mpeg 1 xxx post injury sham2; Danio rerio; RNA Seq,GSM2668097,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668097,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,mpeg_1dpi_sham2_R1.fastq.gz mpeg_1dpi_sham2_R2.fastq.gz,fastq fastq,14052650652.0,88376646.0,GSM2668097 r1,0:79.50 1:79.50,A:4126576983;C:3017594179;G:3122815728;T:3783988637;N:1675125,79,79,,,4126576983,3017594179,3122815728,3783988637,1675125,SRX2918446,SRS2284453,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.90317,0.90144,0.09764,0.10054,0.82714,0.83088,0.45243,0.46936,80,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42524,SRR5683292,SRX2918445,SRS2284454,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 1 xxx post injury sham1,GSM2668096,,source name:Mpeg 1 xxx post injury sham1|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,Mpeg 1 xxx post injury sham1  ,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 1 xxx post injury sham1  ,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,GSM2668096,GSM2668096: Mpeg 1 xxx post injury sham1  ; Danio rerio; RNA Seq,GSM2668096,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668096,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,mpeg_1dpi_sham1_R1.fastq.gz mpeg_1dpi_sham1_R2.fastq.gz,fastq fastq,7915875034.0,49807715.0,GSM2668096 r1,0:79.47 1:79.46,A:2336098216;C:1599111229;G:1685489518;T:2293887279;N:1288792,79,79,,,2336098216,1599111229,1685489518,2293887279,1288792,SRX2918445,SRS2284454,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.86023,0.86553,0.15948,0.1498,0.84258,0.8434,0.46511,0.46972,80,79,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
51253,SRR8632333,SRX5431034,SRS4411029,SRP186864,PRJNA524286,The miR 199 CDK2 axis modulates neutrophil migration and systemic inflammation,GSE127174,Transcriptome Analysis,We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 199 in neutrophils Overall design: for miRNA profiles  we compared the miRNA present in zebrafish neutrophils and keratinocytes to the whole embryo. for miR 199 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR199 or vector control,,pubmed:31451657,,miR 199 3,GSM3629728,,source name:neutrophils overexpressing miR199|strain background:AB|gentoype/variation:overexpressing miR199|tissue:neutrophils,miR 199 3,"Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000 for Samples 6 11. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter:  for Samples 1 5:  “  alignEndsType EndToEnd   outFilterMismatchNmax 1   outFilterMultimapScoreRange 0   outFilterMultimapNmax 10   outSAMunmapped Within   outFilterScoreMinOverLread 0   outFilterMatchNminOverLread 0   outFilterMatchNmin 16   alignSJDBoverhangMin 1000”  for Samples 6 11: “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  “ s 1 –Q 10”  for Samples 6 11  "" p  Q 10"". The data was filtered: for Samples 1 5 using read count > 10 in more than 1 of the samples;  for Samples 6 11  using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts",neutrophils overexpressing miR199,transgenic zebrafish lines were used to produce embryos. For miRNA profiling  transgenic lines expressing GFP in either neutrophils or apical keratincyes were used. For miR 199 target discovery  transgenic lines expressing miR 199 or a vector control together with a GFP reporter were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish embryos were grown to 3 dpf in embryonic media,strain background:AB|gentoype/variation:overexpressing miR199|tissue:neutrophils,GSM3629728,GSM3629728: miR 199 3; Danio rerio; RNA Seq,GSM3629728,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM3629728,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP186864,,,199-3_S24_L003_R1_001.fastq.gz 199-3_S24_L003_R2_001.fastq.gz,fastq fastq,4220702408.0,27767779.0,GSM3629728 r1,0:76 1:76,A:1146580683;C:960484877;G:940832942;T:1172384006;N:419900,76,76,,,1146580683,960484877,940832942,1172384006,419900,SRX5431034,SRS4411029,SRA852308,GEO,"Department of Biological Sciences, Purdue University",2,0.89723,0.89774,0.11975,0.12234,0.7751,0.77922,0.44498,0.44774,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,smartseq,,United States,2019-02-26,Larval,Larval,Blood,Hematopoietic System
51254,SRR8632332,SRX5431033,SRS4411028,SRP186864,PRJNA524286,The miR 199 CDK2 axis modulates neutrophil migration and systemic inflammation,GSE127174,Transcriptome Analysis,We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 199 in neutrophils Overall design: for miRNA profiles  we compared the miRNA present in zebrafish neutrophils and keratinocytes to the whole embryo. for miR 199 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR199 or vector control,,pubmed:31451657,,miR 199 2,GSM3629727,,source name:neutrophils overexpressing miR199|strain background:AB|gentoype/variation:overexpressing miR199|tissue:neutrophils,miR 199 2,"Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000 for Samples 6 11. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter:  for Samples 1 5:  “  alignEndsType EndToEnd   outFilterMismatchNmax 1   outFilterMultimapScoreRange 0   outFilterMultimapNmax 10   outSAMunmapped Within   outFilterScoreMinOverLread 0   outFilterMatchNminOverLread 0   outFilterMatchNmin 16   alignSJDBoverhangMin 1000”  for Samples 6 11: “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  “ s 1 –Q 10”  for Samples 6 11  "" p  Q 10"". The data was filtered: for Samples 1 5 using read count > 10 in more than 1 of the samples;  for Samples 6 11  using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts",neutrophils overexpressing miR199,transgenic zebrafish lines were used to produce embryos. For miRNA profiling  transgenic lines expressing GFP in either neutrophils or apical keratincyes were used. For miR 199 target discovery  transgenic lines expressing miR 199 or a vector control together with a GFP reporter were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish embryos were grown to 3 dpf in embryonic media,strain background:AB|gentoype/variation:overexpressing miR199|tissue:neutrophils,GSM3629727,GSM3629727: miR 199 2; Danio rerio; RNA Seq,GSM3629727,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM3629727,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP186864,,,199-2_S23_L003_R1_001.fastq.gz 199-2_S23_L003_R2_001.fastq.gz,fastq fastq,3774196024.0,24830237.0,GSM3629727 r1,0:76 1:76,A:1021471524;C:862938363;G:846398406;T:1043017523;N:370208,76,76,,,1021471524,862938363,846398406,1043017523,370208,SRX5431033,SRS4411028,SRA852308,GEO,"Department of Biological Sciences, Purdue University",2,0.89642,0.89638,0.09057,0.09272,0.77512,0.78058,0.44281,0.44275,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,smartseq,,United States,2019-02-26,Larval,Larval,Blood,Hematopoietic System
51255,SRR8632331,SRX5431032,SRS4411027,SRP186864,PRJNA524286,The miR 199 CDK2 axis modulates neutrophil migration and systemic inflammation,GSE127174,Transcriptome Analysis,We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 199 in neutrophils Overall design: for miRNA profiles  we compared the miRNA present in zebrafish neutrophils and keratinocytes to the whole embryo. for miR 199 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR199 or vector control,,pubmed:31451657,,miR 199 1,GSM3629726,,source name:neutrophils overexpressing miR199|strain background:AB|gentoype/variation:overexpressing miR199|tissue:neutrophils,miR 199 1,"Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000 for Samples 6 11. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter:  for Samples 1 5:  “  alignEndsType EndToEnd   outFilterMismatchNmax 1   outFilterMultimapScoreRange 0   outFilterMultimapNmax 10   outSAMunmapped Within   outFilterScoreMinOverLread 0   outFilterMatchNminOverLread 0   outFilterMatchNmin 16   alignSJDBoverhangMin 1000”  for Samples 6 11: “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  “ s 1 –Q 10”  for Samples 6 11  "" p  Q 10"". The data was filtered: for Samples 1 5 using read count > 10 in more than 1 of the samples;  for Samples 6 11  using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts",neutrophils overexpressing miR199,transgenic zebrafish lines were used to produce embryos. For miRNA profiling  transgenic lines expressing GFP in either neutrophils or apical keratincyes were used. For miR 199 target discovery  transgenic lines expressing miR 199 or a vector control together with a GFP reporter were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish embryos were grown to 3 dpf in embryonic media,strain background:AB|gentoype/variation:overexpressing miR199|tissue:neutrophils,GSM3629726,GSM3629726: miR 199 1; Danio rerio; RNA Seq,GSM3629726,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM3629726,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP186864,,,199-1_S22_L003_R1_001.fastq.gz 199-1_S22_L003_R2_001.fastq.gz,fastq fastq,4421886720.0,29091360.0,GSM3629726 r1,0:76 1:76,A:1191230633;C:1016736078;G:997138231;T:1216372578;N:409200,76,76,,,1191230633,1016736078,997138231,1216372578,409200,SRX5431032,SRS4411027,SRA852308,GEO,"Department of Biological Sciences, Purdue University",2,0.89934,0.89871,0.09142,0.09283,0.77534,0.77908,0.43477,0.43856,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,smartseq,,United States,2019-02-26,Larval,Larval,Blood,Hematopoietic System
51256,SRR8632330,SRX5431031,SRS4411026,SRP186864,PRJNA524286,The miR 199 CDK2 axis modulates neutrophil migration and systemic inflammation,GSE127174,Transcriptome Analysis,We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 199 in neutrophils Overall design: for miRNA profiles  we compared the miRNA present in zebrafish neutrophils and keratinocytes to the whole embryo. for miR 199 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR199 or vector control,,pubmed:31451657,,vector  3,GSM3629725,,source name:neutrophils vector|strain background:AB|gentoype/variation:overexpressing vector|tissue:neutrophils,vector  3,"Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000 for Samples 6 11. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter:  for Samples 1 5:  “  alignEndsType EndToEnd   outFilterMismatchNmax 1   outFilterMultimapScoreRange 0   outFilterMultimapNmax 10   outSAMunmapped Within   outFilterScoreMinOverLread 0   outFilterMatchNminOverLread 0   outFilterMatchNmin 16   alignSJDBoverhangMin 1000”  for Samples 6 11: “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  “ s 1 –Q 10”  for Samples 6 11  "" p  Q 10"". The data was filtered: for Samples 1 5 using read count > 10 in more than 1 of the samples;  for Samples 6 11  using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts",neutrophils vector,transgenic zebrafish lines were used to produce embryos. For miRNA profiling  transgenic lines expressing GFP in either neutrophils or apical keratincyes were used. For miR 199 target discovery  transgenic lines expressing miR 199 or a vector control together with a GFP reporter were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish embryos were grown to 3 dpf in embryonic media,strain background:AB|gentoype/variation:overexpressing vector|tissue:neutrophils,GSM3629725,GSM3629725: vector  3; Danio rerio; RNA Seq,GSM3629725,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM3629725,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP186864,,,,,4424857712.0,29110906.0,GSM3629725 r1,0:76 1:76,A:1191316852;C:1019584233;G:996921889;T:1216588857;N:445881,76,76,,,1191316852,1019584233,996921889,1216588857,445881,SRX5431031,SRS4411026,SRA852308,GEO,"Department of Biological Sciences, Purdue University",2,0.88192,0.88119,0.09054,0.09305,0.78748,0.79293,0.43612,0.44321,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,smartseq,,United States,2019-02-26,Larval,Larval,Blood,Hematopoietic System
51257,SRR8632328,SRX5431029,SRS4411024,SRP186864,PRJNA524286,The miR 199 CDK2 axis modulates neutrophil migration and systemic inflammation,GSE127174,Transcriptome Analysis,We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 199 in neutrophils Overall design: for miRNA profiles  we compared the miRNA present in zebrafish neutrophils and keratinocytes to the whole embryo. for miR 199 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR199 or vector control,,pubmed:31451657,,vector  1,GSM3629723,,source name:neutrophils vector|strain background:AB|gentoype/variation:overexpressing vector|tissue:neutrophils,vector  1,"Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000 for Samples 6 11. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter:  for Samples 1 5:  “  alignEndsType EndToEnd   outFilterMismatchNmax 1   outFilterMultimapScoreRange 0   outFilterMultimapNmax 10   outSAMunmapped Within   outFilterScoreMinOverLread 0   outFilterMatchNminOverLread 0   outFilterMatchNmin 16   alignSJDBoverhangMin 1000”  for Samples 6 11: “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  “ s 1 –Q 10”  for Samples 6 11  "" p  Q 10"". The data was filtered: for Samples 1 5 using read count > 10 in more than 1 of the samples;  for Samples 6 11  using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts",neutrophils vector,transgenic zebrafish lines were used to produce embryos. For miRNA profiling  transgenic lines expressing GFP in either neutrophils or apical keratincyes were used. For miR 199 target discovery  transgenic lines expressing miR 199 or a vector control together with a GFP reporter were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish embryos were grown to 3 dpf in embryonic media,strain background:AB|gentoype/variation:overexpressing vector|tissue:neutrophils,GSM3629723,GSM3629723: vector  1; Danio rerio; RNA Seq,GSM3629723,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM3629723,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP186864,,,,,5150699360.0,33886180.0,GSM3629723 r1,0:76 1:76,A:1387770699;C:1183384663;G:1159850071;T:1419171313;N:522614,76,76,,,1387770699,1183384663,1159850071,1419171313,522614,SRX5431029,SRS4411024,SRA852308,GEO,"Department of Biological Sciences, Purdue University",2,0.88412,0.88386,0.09124,0.09316,0.78405,0.78817,0.44964,0.44745,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,smartseq,,United States,2019-02-26,Larval,Larval,Blood,Hematopoietic System
51262,SRR8632323,SRX5431024,SRS4411019,SRP186864,PRJNA524286,The miR 199 CDK2 axis modulates neutrophil migration and systemic inflammation,GSE127174,Transcriptome Analysis,We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 199 in neutrophils Overall design: for miRNA profiles  we compared the miRNA present in zebrafish neutrophils and keratinocytes to the whole embryo. for miR 199 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR199 or vector control,,pubmed:31451657,,lyzC+,GSM3629718,,source name:neutrophils|strain background:AB|gentoype/variation:wild type|tissue:neutrophils,lyzC+,"Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000 for Samples 6 11. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter:  for Samples 1 5:  “  alignEndsType EndToEnd   outFilterMismatchNmax 1   outFilterMultimapScoreRange 0   outFilterMultimapNmax 10   outSAMunmapped Within   outFilterScoreMinOverLread 0   outFilterMatchNminOverLread 0   outFilterMatchNmin 16   alignSJDBoverhangMin 1000”  for Samples 6 11: “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  “ s 1 –Q 10”  for Samples 6 11  "" p  Q 10"". The data was filtered: for Samples 1 5 using read count > 10 in more than 1 of the samples;  for Samples 6 11  using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts",neutrophils,transgenic zebrafish lines were used to produce embryos. For miRNA profiling  transgenic lines expressing GFP in either neutrophils or apical keratincyes were used. For miR 199 target discovery  transgenic lines expressing miR 199 or a vector control together with a GFP reporter were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish embryos were grown to 3 dpf in embryonic media,strain background:AB|gentoype/variation:wild type|tissue:neutrophils,GSM3629718,GSM3629718: lyzC+; Danio rerio; RNA Seq,GSM3629718,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM3629718,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP186864,,,lyzc.fastq.gz,fastq,98774200.0,1975484.0,GSM3629718 r1,0:50,A:18442541;C:23267011;G:29755652;T:27302395;N:6601,50,,,,18442541,23267011,29755652,27302395,6601,SRX5431024,SRS4411019,SRA852308,GEO,"Department of Biological Sciences, Purdue University",1,0.24185,,0.03969,,0.94708,,0.65078,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,smartseq,,United States,2019-02-26,Larval,Larval,Blood,Hematopoietic System
56668,SRR13842886,SRX10221255,SRS8374674,SRP247522,PRJNA605187,miR 99 overexpression modulates neutrophil migration,GSE144873,Transcriptome Analysis,We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 99 in neutrophils Overall design: For miR 99 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR1 99 or vector control **Please note that the duplicated vector* sample records of GSE127174 samples have been created as the samples have been re used in the current study and for the convenient retrieval of the complete raw data from SRA.,,,,Vector  2,GSM5129846,,tissue:neutrophils|cell type:neutrophils|genotype/variation:overexpressing vector,Vector  2,Base calling and quality scoreing were performed by Real Time Analysis RTA v2 The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: “ p –Q 10” The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts,neutrophils,transgenic zebrafish lines were used to produce embryos. For miR 99 target discovery  transgenic lines expressing miR 99 or a vector control together with a GFP reporter were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish embryos were grow to 3 dpf in embryonic media,cell type:neutrophils|genotype/variation:overexpressing vector,GSM5129846,GSM5129846: Vector  2; Danio rerio; RNA Seq,GSM5129846,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM5129846,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP247522,,,V-2_S14_L003_R1_001.fastq.gz V-2_S14_L003_R2_001.fastq.gz,fastq fastq,3757553544.0,24720747.0,GSM5129846 r1,0:76 1:76,A:1012476170;C:864162299;G:843777361;T:1036759305;N:378409,76,76,,,1012476170,864162299,843777361,1036759305,378409,SRX10221255,SRS8374674,SRA1039054,GEO,"Department of Biological Sciences, Purdue University",2,0.90022,0.90123,0.10428,0.10723,0.79498,0.79882,0.43947,0.42403,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,sc,single_cell_plate,smartseq,,United States,2021-03-03,Larval,Larval,Blood,Hematopoietic System
56669,SRR11035191,SRX7687418,SRS6113888,SRP247522,PRJNA605187,miR 99 overexpression modulates neutrophil migration,GSE144873,Transcriptome Analysis,We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 99 in neutrophils Overall design: For miR 99 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR1 99 or vector control **Please note that the duplicated vector* sample records of GSE127174 samples have been created as the samples have been re used in the current study and for the convenient retrieval of the complete raw data from SRA.,,,,vector  3 [re used],GSM4299825,,tissue:vector neutrophils|genotype/variation:overexpressing vector|cell type:neutrophils,vector  3 [re used],"Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  “ s 1 –Q 10”  for Samples 6 11  "" p  Q 10"". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts",vector neutrophils,transgenic zebrafish lines were used to produce embryos. For miR 99 target discovery  transgenic lines expressing miR 99 or a vector control together with a GFP reporter were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish embryos were grow to 3 dpf in embryonic media,genotype/variation:overexpressing vector|cell type:neutrophils,GSM4299825,GSM4299825: vector  3 [re used]; Danio rerio; RNA Seq,GSM4299825,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM4299825,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP247522,,,V-3_S15_L003_R1_001.fastq V-3_S15_L003_R2_001.fastq,fastq fastq,4424857712.0,29110906.0,GSM4299825 r1,0:76 1:76,A:1191316852;C:1019584233;G:996921889;T:1216588857;N:445881,76,76,,,1191316852,1019584233,996921889,1216588857,445881,SRX7687418,SRS6113888,SRA1039054,GEO,"Department of Biological Sciences, Purdue University",2,0.88198,0.88112,0.09061,0.09281,0.78778,0.79251,0.43625,0.44314,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,sc,single_cell_plate,smartseq,,United States,2020-02-06,Larval,Larval,Blood,Hematopoietic System
56670,SRR11035190,SRX7687417,SRS6113887,SRP247522,PRJNA605187,miR 99 overexpression modulates neutrophil migration,GSE144873,Transcriptome Analysis,We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 99 in neutrophils Overall design: For miR 99 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR1 99 or vector control **Please note that the duplicated vector* sample records of GSE127174 samples have been created as the samples have been re used in the current study and for the convenient retrieval of the complete raw data from SRA.,,,,vector  1 [re used],GSM4299824,,tissue:vector neutrophils|genotype/variation:overexpressing vector|cell type:neutrophils,vector  1 [re used],"Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  “ s 1 –Q 10”  for Samples 6 11  "" p  Q 10"". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts",vector neutrophils,transgenic zebrafish lines were used to produce embryos. For miR 99 target discovery  transgenic lines expressing miR 99 or a vector control together with a GFP reporter were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish embryos were grow to 3 dpf in embryonic media,genotype/variation:overexpressing vector|cell type:neutrophils,GSM4299824,GSM4299824: vector  1 [re used]; Danio rerio; RNA Seq,GSM4299824,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM4299824,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP247522,,,V-1_S13_L003_R2_001.fastq V-1_S13_L003_R1_001.fastq,fastq fastq,5150699360.0,33886180.0,GSM4299824 r1,0:76 1:76,A:1387770699;C:1183384663;G:1159850071;T:1419171313;N:522614,76,76,,,1387770699,1183384663,1159850071,1419171313,522614,SRX7687417,SRS6113887,SRA1039054,GEO,"Department of Biological Sciences, Purdue University",2,0.88408,0.88384,0.09123,0.09313,0.78374,0.78837,0.45017,0.44717,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,sc,single_cell_plate,smartseq,,United States,2020-02-06,Larval,Larval,Blood,Hematopoietic System
56671,SRR11035189,SRX7687416,SRS6113886,SRP247522,PRJNA605187,miR 99 overexpression modulates neutrophil migration,GSE144873,Transcriptome Analysis,We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 99 in neutrophils Overall design: For miR 99 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR1 99 or vector control **Please note that the duplicated vector* sample records of GSE127174 samples have been created as the samples have been re used in the current study and for the convenient retrieval of the complete raw data from SRA.,,,,miR 99 3,GSM4299823,,tissue:miR 99 neutrophils|genotype/variation:overexpressing miR 99|cell type:neutrophils,miR 99 3,"Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  “ s 1 –Q 10”  for Samples 6 11  "" p  Q 10"". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts",miR 99 neutrophils,transgenic zebrafish lines were used to produce embryos. For miR 99 target discovery  transgenic lines expressing miR 99 or a vector control together with a GFP reporter were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish embryos were grow to 3 dpf in embryonic media,genotype/variation:overexpressing miR 99|cell type:neutrophils,GSM4299823,GSM4299823: miR 99 3; Danio rerio; RNA Seq,GSM4299823,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM4299823,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP247522,,,99-3_S21_L003_R2_001.fastq.gz 99-3_S21_L003_R1_001.fastq.gz,fastq fastq,4537032344.0,29848897.0,GSM4299823 r1,0:76 1:76,A:1221509254;C:1042930118;G:1023047713;T:1249089866;N:455393,76,76,,,1221509254,1042930118,1023047713,1249089866,455393,SRX7687416,SRS6113886,SRA1039054,GEO,"Department of Biological Sciences, Purdue University",2,0.90318,0.90222,0.09091,0.09217,0.79411,0.79793,0.41754,0.42183,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,sc,single_cell_plate,smartseq,,United States,2020-02-06,Larval,Larval,Blood,Hematopoietic System
56672,SRR11035188,SRX7687415,SRS6113885,SRP247522,PRJNA605187,miR 99 overexpression modulates neutrophil migration,GSE144873,Transcriptome Analysis,We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 99 in neutrophils Overall design: For miR 99 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR1 99 or vector control **Please note that the duplicated vector* sample records of GSE127174 samples have been created as the samples have been re used in the current study and for the convenient retrieval of the complete raw data from SRA.,,,,miR 99 2,GSM4299822,,tissue:miR 99 neutrophils|genotype/variation:overexpressing miR 99|cell type:neutrophils,miR 99 2,"Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  “ s 1 –Q 10”  for Samples 6 11  "" p  Q 10"". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts",miR 99 neutrophils,transgenic zebrafish lines were used to produce embryos. For miR 99 target discovery  transgenic lines expressing miR 99 or a vector control together with a GFP reporter were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish embryos were grow to 3 dpf in embryonic media,genotype/variation:overexpressing miR 99|cell type:neutrophils,GSM4299822,GSM4299822: miR 99 2; Danio rerio; RNA Seq,GSM4299822,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM4299822,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP247522,,,99-2_S20_L003_R2_001.fastq.gz 99-2_S20_L003_R1_001.fastq.gz,fastq fastq,3758474512.0,24726806.0,GSM4299822 r1,0:76 1:76,A:1012736859;C:862863675;G:847135976;T:1035362742;N:375260,76,76,,,1012736859,862863675,847135976,1035362742,375260,SRX7687415,SRS6113885,SRA1039054,GEO,"Department of Biological Sciences, Purdue University",2,0.90422,0.90394,0.09824,0.10019,0.79295,0.79644,0.41246,0.42006,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,sc,single_cell_plate,smartseq,,United States,2020-02-06,Larval,Larval,Blood,Hematopoietic System
56673,SRR11035187,SRX7687414,SRS6113884,SRP247522,PRJNA605187,miR 99 overexpression modulates neutrophil migration,GSE144873,Transcriptome Analysis,We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 99 in neutrophils Overall design: For miR 99 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR1 99 or vector control **Please note that the duplicated vector* sample records of GSE127174 samples have been created as the samples have been re used in the current study and for the convenient retrieval of the complete raw data from SRA.,,,,miR 99 1,GSM4299821,,tissue:miR 99 neutrophils|genotype/variation:overexpressing miR 99|cell type:neutrophils,miR 99 1,"Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  “ s 1 –Q 10”  for Samples 6 11  "" p  Q 10"". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts",miR 99 neutrophils,transgenic zebrafish lines were used to produce embryos. For miR 99 target discovery  transgenic lines expressing miR 99 or a vector control together with a GFP reporter were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish embryos were grow to 3 dpf in embryonic media,genotype/variation:overexpressing miR 99|cell type:neutrophils,GSM4299821,GSM4299821: miR 99 1; Danio rerio; RNA Seq,GSM4299821,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM4299821,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP247522,,,99-1_S19_L003_R1_001.fastq.gz 99-1_S19_L003_R2_001.fastq.gz,fastq fastq,4160704056.0,27373053.0,GSM4299821 r1,0:76 1:76,A:1121170591;C:955488866;G:936977987;T:1146641997;N:424615,76,76,,,1121170591,955488866,936977987,1146641997,424615,SRX7687414,SRS6113884,SRA1039054,GEO,"Department of Biological Sciences, Purdue University",2,0.9007,0.89892,0.10574,0.10747,0.79312,0.79768,0.42626,0.42782,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,sc,single_cell_plate,smartseq,,United States,2020-02-06,Larval,Larval,Blood,Hematopoietic System
63408,SRR13785103,SRX10170285,SRS8320380,SRP308232,PRJNA704949,miRNA overexpression modulates neutrophil migration,GSE167554,Transcriptome Analysis,We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 31  miRNA 190 and miRNA 375  in neutrophils Overall design: For miRNA target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR 31  190  375 or vector control,,,,miR 375 2,GSM5107441,,tissue:neutrophils|transgenic line:miR 375,miR 375 2,Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina NovaSeq 6000 The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: “ s 0  p –Q 10” The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts,neutrophils,transgenic zebrafish lines were used to produce embryos. For miRNA target discovery  transgenic lines expressing miR 31  190  375 or a vector control together with a GFP reporter were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish embryos were grow to 3 dpf in embryonic media,transgenic line:miR 375,GSM5107441,GSM5107441: miR 375 2; Danio rerio; RNA Seq,GSM5107441,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM5107441,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP308232,,,11_S27_R1_001.fastq.gz 11_S27_R2_001.fastq.gz,fastq fastq,6029914928.0,29851064.0,GSM5107441 r1,0:101 1:101,A:1615847350;C:1389005627;G:1392538803;T:1632327057;N:196091,101,101,,,1615847350,1389005627,1392538803,1632327057,196091,SRX10170285,SRS8320380,SRA1200205,GEO,"Department of Biological Sciences, Purdue University",2,0.70139,0.70178,0.12251,0.1232,0.84997,0.84956,0.64095,0.63987,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,sc,single_cell_plate,smartseq,,United States,2021-02-25,Larval,Larval,Blood,Hematopoietic System
63409,SRR13785102,SRX10170284,SRS8320379,SRP308232,PRJNA704949,miRNA overexpression modulates neutrophil migration,GSE167554,Transcriptome Analysis,We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 31  miRNA 190 and miRNA 375  in neutrophils Overall design: For miRNA target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR 31  190  375 or vector control,,,,miR 375 1,GSM5107440,,tissue:neutrophils|transgenic line:miR 375,miR 375 1,Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina NovaSeq 6000 The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: “ s 0  p –Q 10” The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts,neutrophils,transgenic zebrafish lines were used to produce embryos. For miRNA target discovery  transgenic lines expressing miR 31  190  375 or a vector control together with a GFP reporter were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish embryos were grow to 3 dpf in embryonic media,transgenic line:miR 375,GSM5107440,GSM5107440: miR 375 1; Danio rerio; RNA Seq,GSM5107440,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM5107440,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP308232,,,10_S26_R1_001.fastq.gz 10_S26_R2_001.fastq.gz,fastq fastq,4592486968.0,22735084.0,GSM5107440 r1,0:101 1:101,A:1227339030;C:1060646304;G:1065493203;T:1238859749;N:148682,101,101,,,1227339030,1060646304,1065493203,1238859749,148682,SRX10170284,SRS8320379,SRA1200205,GEO,"Department of Biological Sciences, Purdue University",2,0.60112,0.60106,0.11798,0.11738,0.85202,0.85352,0.63903,0.63997,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,sc,single_cell_plate,smartseq,,United States,2021-02-25,Larval,Larval,Blood,Hematopoietic System
63410,SRR13785101,SRX10170283,SRS8320378,SRP308232,PRJNA704949,miRNA overexpression modulates neutrophil migration,GSE167554,Transcriptome Analysis,We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 31  miRNA 190 and miRNA 375  in neutrophils Overall design: For miRNA target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR 31  190  375 or vector control,,,,miR 190 2,GSM5107439,,tissue:neutrophils|transgenic line:miR 190,miR 190 2,Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina NovaSeq 6000 The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: “ s 0  p –Q 10” The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts,neutrophils,transgenic zebrafish lines were used to produce embryos. For miRNA target discovery  transgenic lines expressing miR 31  190  375 or a vector control together with a GFP reporter were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish embryos were grow to 3 dpf in embryonic media,transgenic line:miR 190,GSM5107439,GSM5107439: miR 190 2; Danio rerio; RNA Seq,GSM5107439,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM5107439,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP308232,,,8_S24_R1_001.fastq.gz 8_S24_R2_001.fastq.gz,fastq fastq,8568406306.0,42417853.0,GSM5107439 r1,0:101 1:101,A:2236090427;C:2041198943;G:2027464666;T:2263375416;N:276854,101,101,,,2236090427,2041198943,2027464666,2263375416,276854,SRX10170283,SRS8320378,SRA1200205,GEO,"Department of Biological Sciences, Purdue University",2,0.60667,0.60632,0.10166,0.1014,0.84141,0.84001,0.59118,0.58516,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,sc,single_cell_plate,smartseq,,United States,2021-02-25,Larval,Larval,Blood,Hematopoietic System
63411,SRR13785100,SRX10170282,SRS8320377,SRP308232,PRJNA704949,miRNA overexpression modulates neutrophil migration,GSE167554,Transcriptome Analysis,We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 31  miRNA 190 and miRNA 375  in neutrophils Overall design: For miRNA target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR 31  190  375 or vector control,,,,miR 190 1,GSM5107438,,tissue:neutrophils|transgenic line:miR 190,miR 190 1,Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina NovaSeq 6000 The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: “ s 0  p –Q 10” The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts,neutrophils,transgenic zebrafish lines were used to produce embryos. For miRNA target discovery  transgenic lines expressing miR 31  190  375 or a vector control together with a GFP reporter were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish embryos were grow to 3 dpf in embryonic media,transgenic line:miR 190,GSM5107438,GSM5107438: miR 190 1; Danio rerio; RNA Seq,GSM5107438,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM5107438,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP308232,,,7_S23_R1_001.fastq.gz 7_S23_R2_001.fastq.gz,fastq fastq,7761570230.0,38423615.0,GSM5107438 r1,0:101 1:101,A:2071933936;C:1799567237;G:1808478605;T:2081344958;N:245494,101,101,,,2071933936,1799567237,1808478605,2081344958,245494,SRX10170282,SRS8320377,SRA1200205,GEO,"Department of Biological Sciences, Purdue University",2,0.70893,0.70785,0.10171,0.10088,0.81749,0.81649,0.47376,0.47584,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,sc,single_cell_plate,smartseq,,United States,2021-02-25,Larval,Larval,Blood,Hematopoietic System
63412,SRR13785099,SRX10170281,SRS8320376,SRP308232,PRJNA704949,miRNA overexpression modulates neutrophil migration,GSE167554,Transcriptome Analysis,We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 31  miRNA 190 and miRNA 375  in neutrophils Overall design: For miRNA target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR 31  190  375 or vector control,,,,miR 31 3,GSM5107437,,tissue:neutrophils|transgenic line:miR 31,miR 31 3,Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina NovaSeq 6000 The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: “ s 0  p –Q 10” The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts,neutrophils,transgenic zebrafish lines were used to produce embryos. For miRNA target discovery  transgenic lines expressing miR 31  190  375 or a vector control together with a GFP reporter were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish embryos were grow to 3 dpf in embryonic media,transgenic line:miR 31,GSM5107437,GSM5107437: miR 31 3; Danio rerio; RNA Seq,GSM5107437,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM5107437,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP308232,,,6_S22_R1_001.fastq.gz 6_S22_R2_001.fastq.gz,fastq fastq,8612291816.0,42635108.0,GSM5107437 r1,0:101 1:101,A:2355744610;C:1928543523;G:1934674106;T:2393044749;N:284828,101,101,,,2355744610,1928543523,1934674106,2393044749,284828,SRX10170281,SRS8320376,SRA1200205,GEO,"Department of Biological Sciences, Purdue University",2,0.74244,0.74121,0.12601,0.12659,0.82572,0.8268,0.54597,0.54943,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,sc,single_cell_plate,smartseq,,United States,2021-02-25,Larval,Larval,Blood,Hematopoietic System
63413,SRR13785098,SRX10170280,SRS8320375,SRP308232,PRJNA704949,miRNA overexpression modulates neutrophil migration,GSE167554,Transcriptome Analysis,We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 31  miRNA 190 and miRNA 375  in neutrophils Overall design: For miRNA target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR 31  190  375 or vector control,,,,miR 31 1,GSM5107436,,tissue:neutrophils|transgenic line:miR 31,miR 31 1,Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina NovaSeq 6000 The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: “ s 0  p –Q 10” The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts,neutrophils,transgenic zebrafish lines were used to produce embryos. For miRNA target discovery  transgenic lines expressing miR 31  190  375 or a vector control together with a GFP reporter were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish embryos were grow to 3 dpf in embryonic media,transgenic line:miR 31,GSM5107436,GSM5107436: miR 31 1; Danio rerio; RNA Seq,GSM5107436,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM5107436,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP308232,,,4_S20_R1_001.fastq.gz 4_S20_R2_001.fastq.gz,fastq fastq,7552914936.0,37390668.0,GSM5107436 r1,0:101 1:101,A:2067021378;C:1693130222;G:1700053633;T:2092462203;N:247500,101,101,,,2067021378,1693130222,1700053633,2092462203,247500,SRX10170280,SRS8320375,SRA1200205,GEO,"Department of Biological Sciences, Purdue University",2,0.77601,0.77589,0.12034,0.1199,0.80975,0.81097,0.51737,0.51695,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,sc,single_cell_plate,smartseq,,United States,2021-02-25,Larval,Larval,Blood,Hematopoietic System
63414,SRR13785097,SRX10170279,SRS8320374,SRP308232,PRJNA704949,miRNA overexpression modulates neutrophil migration,GSE167554,Transcriptome Analysis,We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 31  miRNA 190 and miRNA 375  in neutrophils Overall design: For miRNA target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR 31  190  375 or vector control,,,,vector 3,GSM5107435,,tissue:neutrophils|transgenic line:vector,vector 3,Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina NovaSeq 6000 The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: “ s 0  p –Q 10” The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts,neutrophils,transgenic zebrafish lines were used to produce embryos. For miRNA target discovery  transgenic lines expressing miR 31  190  375 or a vector control together with a GFP reporter were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish embryos were grow to 3 dpf in embryonic media,transgenic line:vector,GSM5107435,GSM5107435: vector 3; Danio rerio; RNA Seq,GSM5107435,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM5107435,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP308232,,,3_S19_R1_001.fastq.gz 3_S19_R2_001.fastq.gz,fastq fastq,7965811218.0,39434709.0,GSM5107435 r1,0:101 1:101,A:2094197021;C:1873715430;G:1876832073;T:2120806043;N:260651,101,101,,,2094197021,1873715430,1876832073,2120806043,260651,SRX10170279,SRS8320374,SRA1200205,GEO,"Department of Biological Sciences, Purdue University",2,0.54804,0.5496,0.08633,0.08617,0.83465,0.83473,0.56095,0.56097,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,sc,single_cell_plate,smartseq,,United States,2021-02-25,Larval,Larval,Blood,Hematopoietic System
63415,SRR13785096,SRX10170278,SRS8320373,SRP308232,PRJNA704949,miRNA overexpression modulates neutrophil migration,GSE167554,Transcriptome Analysis,We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 31  miRNA 190 and miRNA 375  in neutrophils Overall design: For miRNA target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR 31  190  375 or vector control,,,,vector 2,GSM5107434,,tissue:neutrophils|transgenic line:vector,vector 2,Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina NovaSeq 6000 The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: “ s 0  p –Q 10” The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts,neutrophils,transgenic zebrafish lines were used to produce embryos. For miRNA target discovery  transgenic lines expressing miR 31  190  375 or a vector control together with a GFP reporter were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish embryos were grow to 3 dpf in embryonic media,transgenic line:vector,GSM5107434,GSM5107434: vector 2; Danio rerio; RNA Seq,GSM5107434,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM5107434,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP308232,,,2_S18_R1_001.fastq.gz 2_S18_R2_001.fastq.gz,fastq fastq,7624486566.0,37744983.0,GSM5107434 r1,0:101 1:101,A:2037049856;C:1759511498;G:1765364446;T:2062311110;N:249656,101,101,,,2037049856,1759511498,1765364446,2062311110,249656,SRX10170278,SRS8320373,SRA1200205,GEO,"Department of Biological Sciences, Purdue University",2,0.63672,0.63646,0.11973,0.12018,0.83339,0.83414,0.45361,0.55503,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,sc,single_cell_plate,smartseq,,United States,2021-02-25,Larval,Larval,Blood,Hematopoietic System
63869,SRR14144778,SRX10514122,SRS8637874,SRP313536,PRJNA719817,RORa is required for neutrophil migration,GSE171501,Transcriptome Analysis,We performed RNAseq to identify mRNAs that were specifically down regulated in neutrophils when RORa function is inhibited Overall design: For RORa target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing a dominant RORa or mcherry control,,,,RORaDN 3,GSM5226363,,tissue:neutrophils|cell type:neutrophils|genotype:RORa dominant negative,RORaDN 3,"Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina Novaseq 6000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  “ s 1 –Q 10”  for Samples 6 11  "" p  Q 10"". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts and differential analysis",neutrophils,Transgenic lines expressing RORa dominant negative or mcherry were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish were grow in circulating system,cell type:neutrophils|genotype:RORa dominant negative,GSM5226363,GSM5226363: RORaDN 3; Danio rerio; RNA Seq,GSM5226363,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM5226363,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP313536,,loader:fastq load.py,roraDN-3_S24_R1_001.fastq.gz roraDN-3_S24_R2_001.fastq.gz,fastq fastq,9541970758.0,47237479.0,GSM5226363 r1,0:101 1:101,A:2556115286;C:2215951997;G:2229754627;T:2539986639;N:162209,101,101,,,2556115286,2215951997,2229754627,2539986639,162209,SRX10514122,SRS8637874,SRA1215296,GEO,"Department of Biological Sciences, Purdue University",2,0.94352,0.93947,0.09023,0.08984,0.79224,0.79523,0.45486,0.45588,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,smartseq,,United States,2021-04-05,Adult,Adult,Blood,Hematopoietic System
63870,SRR14144777,SRX10514121,SRS8637873,SRP313536,PRJNA719817,RORa is required for neutrophil migration,GSE171501,Transcriptome Analysis,We performed RNAseq to identify mRNAs that were specifically down regulated in neutrophils when RORa function is inhibited Overall design: For RORa target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing a dominant RORa or mcherry control,,,,RORaDN 2,GSM5226362,,tissue:neutrophils|cell type:neutrophils|genotype:RORa dominant negative,RORaDN 2,"Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina Novaseq 6000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  “ s 1 –Q 10”  for Samples 6 11  "" p  Q 10"". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts and differential analysis",neutrophils,Transgenic lines expressing RORa dominant negative or mcherry were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish were grow in circulating system,cell type:neutrophils|genotype:RORa dominant negative,GSM5226362,GSM5226362: RORaDN 2; Danio rerio; RNA Seq,GSM5226362,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM5226362,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP313536,,loader:fastq load.py,roraDN-2_S23_R1_001.fastq.gz roraDN-2_S23_R2_001.fastq.gz,fastq fastq,7807589466.0,38651433.0,GSM5226362 r1,0:101 1:101,A:2096919144;C:1807670571;G:1821028016;T:2081836449;N:135286,101,101,,,2096919144,1807670571,1821028016,2081836449,135286,SRX10514121,SRS8637873,SRA1215296,GEO,"Department of Biological Sciences, Purdue University",2,0.94042,0.93784,0.09122,0.09133,0.80192,0.80405,0.44224,0.446,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,smartseq,,United States,2021-04-05,Adult,Adult,Blood,Hematopoietic System
63871,SRR14144776,SRX10514120,SRS8637872,SRP313536,PRJNA719817,RORa is required for neutrophil migration,GSE171501,Transcriptome Analysis,We performed RNAseq to identify mRNAs that were specifically down regulated in neutrophils when RORa function is inhibited Overall design: For RORa target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing a dominant RORa or mcherry control,,,,RORaDN 1,GSM5226361,,tissue:neutrophils|cell type:neutrophils|genotype:RORa dominant negative,RORaDN 1,"Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina Novaseq 6000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  “ s 1 –Q 10”  for Samples 6 11  "" p  Q 10"". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts and differential analysis",neutrophils,Transgenic lines expressing RORa dominant negative or mcherry were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish were grow in circulating system,cell type:neutrophils|genotype:RORa dominant negative,GSM5226361,GSM5226361: RORaDN 1; Danio rerio; RNA Seq,GSM5226361,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM5226361,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP313536,,loader:fastq load.py,roraDN-1_S22_R1_001.fastq.gz roraDN-1_S22_R2_001.fastq.gz,fastq fastq,10197330670.0,50481835.0,GSM5226361 r1,0:101 1:101,A:2788946417;C:2302836921;G:2316790438;T:2788574338;N:182556,101,101,,,2788946417,2302836921,2316790438,2788574338,182556,SRX10514120,SRS8637872,SRA1215296,GEO,"Department of Biological Sciences, Purdue University",2,0.92564,0.92366,0.09078,0.09026,0.81381,0.81542,0.50301,0.49369,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,smartseq,,United States,2021-04-05,Adult,Adult,Blood,Hematopoietic System
63872,SRR14144775,SRX10514119,SRS8637871,SRP313536,PRJNA719817,RORa is required for neutrophil migration,GSE171501,Transcriptome Analysis,We performed RNAseq to identify mRNAs that were specifically down regulated in neutrophils when RORa function is inhibited Overall design: For RORa target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing a dominant RORa or mcherry control,,,,mCherry 3,GSM5226360,,tissue:neutrophils|cell type:neutrophils|genotype:control,mCherry 3,"Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina Novaseq 6000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  “ s 1 –Q 10”  for Samples 6 11  "" p  Q 10"". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts and differential analysis",neutrophils,Transgenic lines expressing RORa dominant negative or mcherry were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish were grow in circulating system,cell type:neutrophils|genotype:control,GSM5226360,GSM5226360: mCherry 3; Danio rerio; RNA Seq,GSM5226360,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM5226360,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP313536,,loader:fastq load.py,ctrl_mcherry-3_S21_R1_001.fastq.gz ctrl_mcherry-3_S21_R2_001.fastq.gz,fastq fastq,8880772036.0,43964218.0,GSM5226360 r1,0:101 1:101,A:2381825109;C:2057122621;G:2068743076;T:2372921245;N:159985,101,101,,,2381825109,2057122621,2068743076,2372921245,159985,SRX10514119,SRS8637871,SRA1215296,GEO,"Department of Biological Sciences, Purdue University",2,0.93299,0.93061,0.09615,0.09601,0.80004,0.8017,0.43695,0.43475,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,smartseq,,United States,2021-04-05,Adult,Adult,Blood,Hematopoietic System
63873,SRR14144774,SRX10514118,SRS8637870,SRP313536,PRJNA719817,RORa is required for neutrophil migration,GSE171501,Transcriptome Analysis,We performed RNAseq to identify mRNAs that were specifically down regulated in neutrophils when RORa function is inhibited Overall design: For RORa target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing a dominant RORa or mcherry control,,,,mCherry 2,GSM5226359,,tissue:neutrophils|cell type:neutrophils|genotype:control,mCherry 2,"Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina Novaseq 6000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  “ s 1 –Q 10”  for Samples 6 11  "" p  Q 10"". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts and differential analysis",neutrophils,Transgenic lines expressing RORa dominant negative or mcherry were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish were grow in circulating system,cell type:neutrophils|genotype:control,GSM5226359,GSM5226359: mCherry 2; Danio rerio; RNA Seq,GSM5226359,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM5226359,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP313536,,loader:fastq load.py,ctrl_mcherry-2_S20_R1_001.fastq.gz ctrl_mcherry-2_S20_R2_001.fastq.gz,fastq fastq,9245210942.0,45768371.0,GSM5226359 r1,0:101 1:101,A:2490401320;C:2130041068;G:2145686856;T:2478916438;N:165260,101,101,,,2490401320,2130041068,2145686856,2478916438,165260,SRX10514118,SRS8637870,SRA1215296,GEO,"Department of Biological Sciences, Purdue University",2,0.93171,0.92876,0.08782,0.08787,0.79699,0.79886,0.44448,0.44757,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,smartseq,,United States,2021-04-05,Adult,Adult,Blood,Hematopoietic System
63874,SRR14144773,SRX10514117,SRS8637869,SRP313536,PRJNA719817,RORa is required for neutrophil migration,GSE171501,Transcriptome Analysis,We performed RNAseq to identify mRNAs that were specifically down regulated in neutrophils when RORa function is inhibited Overall design: For RORa target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing a dominant RORa or mcherry control,,,,mCherry 1,GSM5226358,,tissue:neutrophils|cell type:neutrophils|genotype:control,mCherry 1,"Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina Novaseq 6000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “  outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  “ s 1 –Q 10”  for Samples 6 11  "" p  Q 10"". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts and differential analysis",neutrophils,Transgenic lines expressing RORa dominant negative or mcherry were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,zebrafish were grow in circulating system,cell type:neutrophils|genotype:control,GSM5226358,GSM5226358: mCherry 1; Danio rerio; RNA Seq,GSM5226358,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..,GEO Accession:GSM5226358,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP313536,,loader:fastq load.py,ctrl_mcherry-1_S19_R1_001.fastq.gz ctrl_mcherry-1_S19_R2_001.fastq.gz,fastq fastq,8133040958.0,40262579.0,GSM5226358 r1,0:101 1:101,A:2181019795;C:1885103754;G:1889273889;T:2177502095;N:141425,101,101,,,2181019795,1885103754,1889273889,2177502095,141425,SRX10514117,SRS8637869,SRA1215296,GEO,"Department of Biological Sciences, Purdue University",2,0.9318,0.93011,0.09874,0.09885,0.79239,0.79488,0.42603,0.44023,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,smartseq,,United States,2021-04-05,Adult,Adult,Blood,Hematopoietic System
68662,SRR18124522,SRX14274937,SRS12093628,SRP361285,PRJNA809951,A lysosomal regulatory circuit essential for the development and function of microglia,GSE197349,Transcriptome Analysis,We performed Illumina NovaSeq on macrophages isolated from zebrafish Overall design: Cells of the macrophage lineage tagged with mpeg:GFP were isolated from rraga mutants and their wildtype siblings by FACS  RNA was extracted  and sequencing was performed.,parent bioproject:PRJNA809950,pubmed:36044568,,rraga wildtype sibling macrophage sample biological replicate 4,GSM5914979,,tissue:Macrophages|genotype:rraga wild type|strain:TL|developmental stage:6 dpf type:Macrophages,rraga wildtype sibling macrophage sample biological replicate 4,Raw data of FASTQ format were processed through Novogene in house PERL scripts Clean reads were obtained by removing reads containing adapter  reads containing poly N and low quality reads from raw data Q20  Q30  and GC content of all clean data were calculated Index of reference genome GRCz11 was built using Hisat2 v2.0.5 and paired end clean reads were aligned to reference genome. Mapped reads of each sample were assembled by StringTie v1.3.3b featureCount v1.5.0 was used to count the read numbers mapped to each gene. Differential expression analysis was performed using the DESeq2R package 1.20.0 Genome build: GRCz11 Supplementary files format and content: text file contains gene counts  normalized FPKM reads for genes identified by gene name and ENSEMBL ID,Macrophages,Embryos were scored as mutant or wildtype using a confocal microscope at 4 dpf and 5 dpf Larvae were dissociated at 6 dpf and GFP+ macrophages were isolated using FACS.,RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit,Zebrafish embryos were raised at 28.5 ºC in embryo water with methylene blue and PTU,genotype:rraga wild type|strain:TL|developmental stage:6 dpf type:Macrophages,GSM5914979,GSM5914979: rraga wildtype sibling macrophage sample biological replicate 4; Danio rerio; RNA Seq,GSM5914979 r1,GSM5914979,1,RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP361285,,loader:fastq load.py,WT5_S62_1.fq.gz WT5_S62_2.fq.gz,fastq fastq,14242695000.0,47475650.0,GSM5914979 r1,0:150 1:150,A:3803830606;C:3323851570;G:3342727186;T:3772146235;N:139403,150,150,,,3803830606,3323851570,3342727186,3772146235,139403,SRX14274937,SRS12093628,SRA1377812,"Talbot, Developmental Biology, Stanford University","Talbot, Developmental Biology, Stanford University",2,0.94344,0.94256,0.06598,0.06609,0.74732,0.74933,0.48975,0.48907,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2022-02-24,Larval,Larval,Blood,Hematopoietic System
68663,SRR18124523,SRX14274936,SRS12093627,SRP361285,PRJNA809951,A lysosomal regulatory circuit essential for the development and function of microglia,GSE197349,Transcriptome Analysis,We performed Illumina NovaSeq on macrophages isolated from zebrafish Overall design: Cells of the macrophage lineage tagged with mpeg:GFP were isolated from rraga mutants and their wildtype siblings by FACS  RNA was extracted  and sequencing was performed.,parent bioproject:PRJNA809950,pubmed:36044568,,rraga wildtype sibling macrophage sample biological replicate 3,GSM5914978,,tissue:Macrophages|genotype:rraga wild type|strain:TL|developmental stage:6 dpf type:Macrophages,rraga wildtype sibling macrophage sample biological replicate 3,Raw data of FASTQ format were processed through Novogene in house PERL scripts Clean reads were obtained by removing reads containing adapter  reads containing poly N and low quality reads from raw data Q20  Q30  and GC content of all clean data were calculated Index of reference genome GRCz11 was built using Hisat2 v2.0.5 and paired end clean reads were aligned to reference genome. Mapped reads of each sample were assembled by StringTie v1.3.3b featureCount v1.5.0 was used to count the read numbers mapped to each gene. Differential expression analysis was performed using the DESeq2R package 1.20.0 Genome build: GRCz11 Supplementary files format and content: text file contains gene counts  normalized FPKM reads for genes identified by gene name and ENSEMBL ID,Macrophages,Embryos were scored as mutant or wildtype using a confocal microscope at 4 dpf and 5 dpf Larvae were dissociated at 6 dpf and GFP+ macrophages were isolated using FACS.,RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit,Zebrafish embryos were raised at 28.5 ºC in embryo water with methylene blue and PTU,genotype:rraga wild type|strain:TL|developmental stage:6 dpf type:Macrophages,GSM5914978,GSM5914978: rraga wildtype sibling macrophage sample biological replicate 3; Danio rerio; RNA Seq,GSM5914978 r1,GSM5914978,1,RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP361285,,loader:fastq load.py,WT4_S60_1.fq.gz WT4_S60_2.fq.gz,fastq fastq,13192857000.0,43976190.0,GSM5914978 r1,0:150 1:150,A:3525239825;C:3077994139;G:3094731575;T:3494762519;N:128942,150,150,,,3525239825,3077994139,3094731575,3494762519,128942,SRX14274936,SRS12093627,SRA1377812,"Talbot, Developmental Biology, Stanford University","Talbot, Developmental Biology, Stanford University",2,0.94452,0.94349,0.06316,0.06336,0.75939,0.75986,0.48896,0.48863,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2022-02-24,Larval,Larval,Blood,Hematopoietic System
68664,SRR18124524,SRX14274935,SRS12093626,SRP361285,PRJNA809951,A lysosomal regulatory circuit essential for the development and function of microglia,GSE197349,Transcriptome Analysis,We performed Illumina NovaSeq on macrophages isolated from zebrafish Overall design: Cells of the macrophage lineage tagged with mpeg:GFP were isolated from rraga mutants and their wildtype siblings by FACS  RNA was extracted  and sequencing was performed.,parent bioproject:PRJNA809950,pubmed:36044568,,rraga wildtype sibling macrophage sample biological replicate 2,GSM5914977,,tissue:Macrophages|genotype:rraga wild type|strain:TL|developmental stage:6 dpf type:Macrophages,rraga wildtype sibling macrophage sample biological replicate 2,Raw data of FASTQ format were processed through Novogene in house PERL scripts Clean reads were obtained by removing reads containing adapter  reads containing poly N and low quality reads from raw data Q20  Q30  and GC content of all clean data were calculated Index of reference genome GRCz11 was built using Hisat2 v2.0.5 and paired end clean reads were aligned to reference genome. Mapped reads of each sample were assembled by StringTie v1.3.3b featureCount v1.5.0 was used to count the read numbers mapped to each gene. Differential expression analysis was performed using the DESeq2R package 1.20.0 Genome build: GRCz11 Supplementary files format and content: text file contains gene counts  normalized FPKM reads for genes identified by gene name and ENSEMBL ID,Macrophages,Embryos were scored as mutant or wildtype using a confocal microscope at 4 dpf and 5 dpf Larvae were dissociated at 6 dpf and GFP+ macrophages were isolated using FACS.,RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit,Zebrafish embryos were raised at 28.5 ºC in embryo water with methylene blue and PTU,genotype:rraga wild type|strain:TL|developmental stage:6 dpf type:Macrophages,GSM5914977,GSM5914977: rraga wildtype sibling macrophage sample biological replicate 2; Danio rerio; RNA Seq,GSM5914977 r1,GSM5914977,1,RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP361285,,loader:fastq load.py,WT2_S58_1.fq.gz WT2_S58_2.fq.gz,fastq fastq,14306259300.0,47687531.0,GSM5914977 r1,0:150 1:150,A:3835681757;C:3324696461;G:3339727926;T:3806013274;N:139882,150,150,,,3835681757,3324696461,3339727926,3806013274,139882,SRX14274935,SRS12093626,SRA1377812,"Talbot, Developmental Biology, Stanford University","Talbot, Developmental Biology, Stanford University",2,0.946,0.94382,0.07547,0.07591,0.7529,0.75404,0.4827,0.48954,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2022-02-24,Larval,Larval,Blood,Hematopoietic System
68665,SRR18124525,SRX14274934,SRS12093625,SRP361285,PRJNA809951,A lysosomal regulatory circuit essential for the development and function of microglia,GSE197349,Transcriptome Analysis,We performed Illumina NovaSeq on macrophages isolated from zebrafish Overall design: Cells of the macrophage lineage tagged with mpeg:GFP were isolated from rraga mutants and their wildtype siblings by FACS  RNA was extracted  and sequencing was performed.,parent bioproject:PRJNA809950,pubmed:36044568,,rraga wildtype sibling macrophage sample biological replicate 1,GSM5914976,,tissue:Macrophages|genotype:rraga wild type|strain:TL|developmental stage:6 dpf type:Macrophages,rraga wildtype sibling macrophage sample biological replicate 1,Raw data of FASTQ format were processed through Novogene in house PERL scripts Clean reads were obtained by removing reads containing adapter  reads containing poly N and low quality reads from raw data Q20  Q30  and GC content of all clean data were calculated Index of reference genome GRCz11 was built using Hisat2 v2.0.5 and paired end clean reads were aligned to reference genome. Mapped reads of each sample were assembled by StringTie v1.3.3b featureCount v1.5.0 was used to count the read numbers mapped to each gene. Differential expression analysis was performed using the DESeq2R package 1.20.0 Genome build: GRCz11 Supplementary files format and content: text file contains gene counts  normalized FPKM reads for genes identified by gene name and ENSEMBL ID,Macrophages,Embryos were scored as mutant or wildtype using a confocal microscope at 4 dpf and 5 dpf Larvae were dissociated at 6 dpf and GFP+ macrophages were isolated using FACS.,RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit,Zebrafish embryos were raised at 28.5 ºC in embryo water with methylene blue and PTU,genotype:rraga wild type|strain:TL|developmental stage:6 dpf type:Macrophages,GSM5914976,GSM5914976: rraga wildtype sibling macrophage sample biological replicate 1; Danio rerio; RNA Seq,GSM5914976 r1,GSM5914976,1,RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP361285,,loader:fastq load.py,WT1_S56_1.fq.gz WT1_S56_2.fq.gz,fastq fastq,15108936000.0,50363120.0,GSM5914976 r1,0:150 1:150,A:4018293581;C:3543481365;G:3559406647;T:3987606103;N:148304,150,150,,,4018293581,3543481365,3559406647,3987606103,148304,SRX14274934,SRS12093625,SRA1377812,"Talbot, Developmental Biology, Stanford University","Talbot, Developmental Biology, Stanford University",2,0.94582,0.944,0.06477,0.06488,0.75613,0.75672,0.47628,0.47602,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2022-02-24,Larval,Larval,Blood,Hematopoietic System
68666,SRR18124526,SRX14274933,SRS12093624,SRP361285,PRJNA809951,A lysosomal regulatory circuit essential for the development and function of microglia,GSE197349,Transcriptome Analysis,We performed Illumina NovaSeq on macrophages isolated from zebrafish Overall design: Cells of the macrophage lineage tagged with mpeg:GFP were isolated from rraga mutants and their wildtype siblings by FACS  RNA was extracted  and sequencing was performed.,parent bioproject:PRJNA809950,pubmed:36044568,,rraga mutant macrophage sample biological replicate 4,GSM5914975,,tissue:Macrophages|genotype:rraga mutant|strain:TL|developmental stage:6 dpf type:Macrophages,rraga mutant macrophage sample biological replicate 4,Raw data of FASTQ format were processed through Novogene in house PERL scripts Clean reads were obtained by removing reads containing adapter  reads containing poly N and low quality reads from raw data Q20  Q30  and GC content of all clean data were calculated Index of reference genome GRCz11 was built using Hisat2 v2.0.5 and paired end clean reads were aligned to reference genome. Mapped reads of each sample were assembled by StringTie v1.3.3b featureCount v1.5.0 was used to count the read numbers mapped to each gene. Differential expression analysis was performed using the DESeq2R package 1.20.0 Genome build: GRCz11 Supplementary files format and content: text file contains gene counts  normalized FPKM reads for genes identified by gene name and ENSEMBL ID,Macrophages,Embryos were scored as mutant or wildtype using a confocal microscope at 4 dpf and 5 dpf Larvae were dissociated at 6 dpf and GFP+ macrophages were isolated using FACS.,RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit,Zebrafish embryos were raised at 28.5 ºC in embryo water with methylene blue and PTU,genotype:rraga mutant|strain:TL|developmental stage:6 dpf type:Macrophages,GSM5914975,GSM5914975: rraga mutant macrophage sample biological replicate 4; Danio rerio; RNA Seq,GSM5914975 r1,GSM5914975,1,RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP361285,,loader:fastq load.py,RRGA5_S63_1.fq.gz RRGA5_S63_2.fq.gz,fastq fastq,16056097500.0,53520325.0,GSM5914975 r1,0:150 1:150,A:4294601650;C:3737735522;G:3760015896;T:4263588285;N:156147,150,150,,,4294601650,3737735522,3760015896,4263588285,156147,SRX14274933,SRS12093624,SRA1377812,"Talbot, Developmental Biology, Stanford University","Talbot, Developmental Biology, Stanford University",2,0.94205,0.93992,0.04764,0.04795,0.76278,0.76512,0.48852,0.48702,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2022-02-24,Larval,Larval,Blood,Hematopoietic System
68667,SRR18124527,SRX14274932,SRS12093623,SRP361285,PRJNA809951,A lysosomal regulatory circuit essential for the development and function of microglia,GSE197349,Transcriptome Analysis,We performed Illumina NovaSeq on macrophages isolated from zebrafish Overall design: Cells of the macrophage lineage tagged with mpeg:GFP were isolated from rraga mutants and their wildtype siblings by FACS  RNA was extracted  and sequencing was performed.,parent bioproject:PRJNA809950,pubmed:36044568,,rraga mutant macrophage sample biological replicate 3,GSM5914974,,tissue:Macrophages|genotype:rraga mutant|strain:TL|developmental stage:6 dpf type:Macrophages,rraga mutant macrophage sample biological replicate 3,Raw data of FASTQ format were processed through Novogene in house PERL scripts Clean reads were obtained by removing reads containing adapter  reads containing poly N and low quality reads from raw data Q20  Q30  and GC content of all clean data were calculated Index of reference genome GRCz11 was built using Hisat2 v2.0.5 and paired end clean reads were aligned to reference genome. Mapped reads of each sample were assembled by StringTie v1.3.3b featureCount v1.5.0 was used to count the read numbers mapped to each gene. Differential expression analysis was performed using the DESeq2R package 1.20.0 Genome build: GRCz11 Supplementary files format and content: text file contains gene counts  normalized FPKM reads for genes identified by gene name and ENSEMBL ID,Macrophages,Embryos were scored as mutant or wildtype using a confocal microscope at 4 dpf and 5 dpf Larvae were dissociated at 6 dpf and GFP+ macrophages were isolated using FACS.,RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit,Zebrafish embryos were raised at 28.5 ºC in embryo water with methylene blue and PTU,genotype:rraga mutant|strain:TL|developmental stage:6 dpf type:Macrophages,GSM5914974,GSM5914974: rraga mutant macrophage sample biological replicate 3; Danio rerio; RNA Seq,GSM5914974 r1,GSM5914974,1,RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP361285,,loader:fastq load.py,RRGA4_S61_1.fq.gz RRGA4_S61_2.fq.gz,fastq fastq,13800732900.0,46002443.0,GSM5914974 r1,0:150 1:150,A:3681710812;C:3222984593;G:3240482342;T:3655419422;N:135731,150,150,,,3681710812,3222984593,3240482342,3655419422,135731,SRX14274932,SRS12093623,SRA1377812,"Talbot, Developmental Biology, Stanford University","Talbot, Developmental Biology, Stanford University",2,0.94451,0.94367,0.03979,0.04074,0.7754,0.77654,0.49111,0.48192,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2022-02-24,Larval,Larval,Blood,Hematopoietic System
68668,SRR18124528,SRX14274931,SRS12093622,SRP361285,PRJNA809951,A lysosomal regulatory circuit essential for the development and function of microglia,GSE197349,Transcriptome Analysis,We performed Illumina NovaSeq on macrophages isolated from zebrafish Overall design: Cells of the macrophage lineage tagged with mpeg:GFP were isolated from rraga mutants and their wildtype siblings by FACS  RNA was extracted  and sequencing was performed.,parent bioproject:PRJNA809950,pubmed:36044568,,rraga mutant macrophage sample biological replicate 2,GSM5914973,,tissue:Macrophages|genotype:rraga mutant|strain:TL|developmental stage:6 dpf type:Macrophages,rraga mutant macrophage sample biological replicate 2,Raw data of FASTQ format were processed through Novogene in house PERL scripts Clean reads were obtained by removing reads containing adapter  reads containing poly N and low quality reads from raw data Q20  Q30  and GC content of all clean data were calculated Index of reference genome GRCz11 was built using Hisat2 v2.0.5 and paired end clean reads were aligned to reference genome. Mapped reads of each sample were assembled by StringTie v1.3.3b featureCount v1.5.0 was used to count the read numbers mapped to each gene. Differential expression analysis was performed using the DESeq2R package 1.20.0 Genome build: GRCz11 Supplementary files format and content: text file contains gene counts  normalized FPKM reads for genes identified by gene name and ENSEMBL ID,Macrophages,Embryos were scored as mutant or wildtype using a confocal microscope at 4 dpf and 5 dpf Larvae were dissociated at 6 dpf and GFP+ macrophages were isolated using FACS.,RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit,Zebrafish embryos were raised at 28.5 ºC in embryo water with methylene blue and PTU,genotype:rraga mutant|strain:TL|developmental stage:6 dpf type:Macrophages,GSM5914973,GSM5914973: rraga mutant macrophage sample biological replicate 2; Danio rerio; RNA Seq,GSM5914973 r1,GSM5914973,1,RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP361285,,loader:fastq load.py,RRGA2_S59_1.fq.gz RRGA2_S59_2.fq.gz,fastq fastq,13029428100.0,43431427.0,GSM5914973 r1,0:150 1:150,A:3511989568;C:3007102768;G:3023337404;T:3486872579;N:125781,150,150,,,3511989568,3007102768,3023337404,3486872579,125781,SRX14274931,SRS12093622,SRA1377812,"Talbot, Developmental Biology, Stanford University","Talbot, Developmental Biology, Stanford University",2,0.94027,0.93791,0.05191,0.05248,0.77759,0.77908,0.48627,0.49588,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2022-02-24,Larval,Larval,Blood,Hematopoietic System
68669,SRR18124529,SRX14274930,SRS12093621,SRP361285,PRJNA809951,A lysosomal regulatory circuit essential for the development and function of microglia,GSE197349,Transcriptome Analysis,We performed Illumina NovaSeq on macrophages isolated from zebrafish Overall design: Cells of the macrophage lineage tagged with mpeg:GFP were isolated from rraga mutants and their wildtype siblings by FACS  RNA was extracted  and sequencing was performed.,parent bioproject:PRJNA809950,pubmed:36044568,,rraga mutant macrophage sample biological replicate 1,GSM5914972,,tissue:Macrophages|genotype:rraga mutant|strain:TL|developmental stage:6 dpf type:Macrophages,rraga mutant macrophage sample biological replicate 1,Raw data of FASTQ format were processed through Novogene in house PERL scripts Clean reads were obtained by removing reads containing adapter  reads containing poly N and low quality reads from raw data Q20  Q30  and GC content of all clean data were calculated Index of reference genome GRCz11 was built using Hisat2 v2.0.5 and paired end clean reads were aligned to reference genome. Mapped reads of each sample were assembled by StringTie v1.3.3b featureCount v1.5.0 was used to count the read numbers mapped to each gene. Differential expression analysis was performed using the DESeq2R package 1.20.0 Genome build: GRCz11 Supplementary files format and content: text file contains gene counts  normalized FPKM reads for genes identified by gene name and ENSEMBL ID,Macrophages,Embryos were scored as mutant or wildtype using a confocal microscope at 4 dpf and 5 dpf Larvae were dissociated at 6 dpf and GFP+ macrophages were isolated using FACS.,RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit,Zebrafish embryos were raised at 28.5 ºC in embryo water with methylene blue and PTU,genotype:rraga mutant|strain:TL|developmental stage:6 dpf type:Macrophages,GSM5914972,GSM5914972: rraga mutant macrophage sample biological replicate 1; Danio rerio; RNA Seq,GSM5914972 r1,GSM5914972,1,RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP361285,,loader:fastq load.py,RRGA1_S57_1.fq.gz RRGA1_S57_2.fq.gz,fastq fastq,15238446600.0,50794822.0,GSM5914972 r1,0:150 1:150,A:4094568173;C:3530048869;G:3550699321;T:4062982708;N:147529,150,150,,,4094568173,3530048869,3550699321,4062982708,147529,SRX14274930,SRS12093621,SRA1377812,"Talbot, Developmental Biology, Stanford University","Talbot, Developmental Biology, Stanford University",2,0.94164,0.9408,0.04872,0.04897,0.76999,0.77029,0.47856,0.48556,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2022-02-24,Larval,Larval,Blood,Hematopoietic System
71860,SRR22135238,SRX18114786,SRS15617125,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,D Emergency granulopoiesis neutrophils  post infection  rep 4,GSM6704384,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,D Emergency granulopoiesis neutrophils  post infection  rep 4,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,GSM6704384,GSM6704384: D Emergency granulopoiesis neutrophils  post infection  rep 4; Danio rerio; RNA Seq,GSM6704384 r1,GSM6704384,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,D4_S16_L001_R1_001.fastq.gz,fastq,492998897.0,6538726.0,GSM6704384 r1,0:75.40,A:142208659;C:103614806;G:105979666;T:141151718;N:44048,75,,,,142208659,103614806,105979666,141151718,44048,SRX18114786,SRS15617125,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.90296,,0.31723,,0.76771,,0.48693,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71861,SRR22135239,SRX18114786,SRS15617125,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,D Emergency granulopoiesis neutrophils  post infection  rep 4,GSM6704384,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,D Emergency granulopoiesis neutrophils  post infection  rep 4,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,GSM6704384,GSM6704384: D Emergency granulopoiesis neutrophils  post infection  rep 4; Danio rerio; RNA Seq,GSM6704384 r1,GSM6704384,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,D4_S16_L002_R1_001.fastq.gz,fastq,486522568.0,6452453.0,GSM6704384 r2,0:75.40,A:140379916;C:102147805;G:104621474;T:139332047;N:41326,75,,,,140379916,102147805,104621474,139332047,41326,SRX18114786,SRS15617125,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.9012,,0.31652,,0.7681,,0.48379,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71862,SRR22135240,SRX18114786,SRS15617125,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,D Emergency granulopoiesis neutrophils  post infection  rep 4,GSM6704384,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,D Emergency granulopoiesis neutrophils  post infection  rep 4,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,GSM6704384,GSM6704384: D Emergency granulopoiesis neutrophils  post infection  rep 4; Danio rerio; RNA Seq,GSM6704384 r1,GSM6704384,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,D4_S16_L003_R1_001.fastq.gz,fastq,499411895.0,6623685.0,GSM6704384 r3,0:75.40,A:144028426;C:105024209;G:107425776;T:142887718;N:45766,75,,,,144028426,105024209,107425776,142887718,45766,SRX18114786,SRS15617125,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.90214,,0.3188,,0.76863,,0.48665,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71863,SRR22135241,SRX18114786,SRS15617125,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,D Emergency granulopoiesis neutrophils  post infection  rep 4,GSM6704384,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,D Emergency granulopoiesis neutrophils  post infection  rep 4,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,GSM6704384,GSM6704384: D Emergency granulopoiesis neutrophils  post infection  rep 4; Danio rerio; RNA Seq,GSM6704384 r1,GSM6704384,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,D4_S16_L004_R1_001.fastq.gz,fastq,491985584.0,6524636.0,GSM6704384 r4,0:75.40,A:142093034;C:103222008;G:105595618;T:141031132;N:43792,75,,,,142093034,103222008,105595618,141031132,43792,SRX18114786,SRS15617125,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.90151,,0.31805,,0.7682,,0.48804,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71864,SRR22135242,SRX18114785,SRS15617124,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,D Emergency granulopoiesis neutrophils  post infection  rep 3,GSM6704383,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,D Emergency granulopoiesis neutrophils  post infection  rep 3,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,GSM6704383,GSM6704383: D Emergency granulopoiesis neutrophils  post infection  rep 3; Danio rerio; RNA Seq,GSM6704383 r1,GSM6704383,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,D3_S15_L001_R1_001.fastq.gz,fastq,501524165.0,6667267.0,GSM6704383 r1,0:75.22,A:143118995;C:106791152;G:109715789;T:141789029;N:109200,75,,,,143118995,106791152,109715789,141789029,109200,SRX18114785,SRS15617124,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.90211,,0.3184,,0.7569,,0.48864,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71865,SRR22135243,SRX18114785,SRS15617124,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,D Emergency granulopoiesis neutrophils  post infection  rep 3,GSM6704383,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,D Emergency granulopoiesis neutrophils  post infection  rep 3,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,GSM6704383,GSM6704383: D Emergency granulopoiesis neutrophils  post infection  rep 3; Danio rerio; RNA Seq,GSM6704383 r1,GSM6704383,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,D3_S15_L002_R1_001.fastq.gz,fastq,494015859.0,6567071.0,GSM6704383 r2,0:75.23,A:140996216;C:105164019;G:108107082;T:139639536;N:109006,75,,,,140996216,105164019,108107082,139639536,109006,SRX18114785,SRS15617124,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.90121,,0.31746,,0.75883,,0.47681,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71866,SRR22135244,SRX18114785,SRS15617124,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,D Emergency granulopoiesis neutrophils  post infection  rep 3,GSM6704383,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,D Emergency granulopoiesis neutrophils  post infection  rep 3,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,GSM6704383,GSM6704383: D Emergency granulopoiesis neutrophils  post infection  rep 3; Danio rerio; RNA Seq,GSM6704383 r1,GSM6704383,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,D3_S15_L003_R1_001.fastq.gz,fastq,508620356.0,6761277.0,GSM6704383 r3,0:75.23,A:145208025;C:108358330;G:111248753;T:143692334;N:112914,75,,,,145208025,108358330,111248753,143692334,112914,SRX18114785,SRS15617124,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.90315,,0.32027,,0.7582,,0.49103,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71867,SRR22135245,SRX18114785,SRS15617124,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,D Emergency granulopoiesis neutrophils  post infection  rep 3,GSM6704383,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,D Emergency granulopoiesis neutrophils  post infection  rep 3,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,GSM6704383,GSM6704383: D Emergency granulopoiesis neutrophils  post infection  rep 3; Danio rerio; RNA Seq,GSM6704383 r1,GSM6704383,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,D3_S15_L004_R1_001.fastq.gz,fastq,502842850.0,6684188.0,GSM6704383 r4,0:75.23,A:143669043;C:106987130;G:109853730;T:142224644;N:108303,75,,,,143669043,106987130,109853730,142224644,108303,SRX18114785,SRS15617124,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.90348,,0.31941,,0.75941,,0.47942,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71868,SRR22135246,SRX18114784,SRS15617123,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,D Emergency granulopoiesis neutrophils  post infection  rep 2,GSM6704382,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,D Emergency granulopoiesis neutrophils  post infection  rep 2,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,GSM6704382,GSM6704382: D Emergency granulopoiesis neutrophils  post infection  rep 2; Danio rerio; RNA Seq,GSM6704382 r1,GSM6704382,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,D2_S14_L001_R1_001.fastq.gz,fastq,623282435.0,8275237.0,GSM6704382 r1,0:75.32,A:174770372;C:136305753;G:139952685;T:172170159;N:83466,75,,,,174770372,136305753,139952685,172170159,83466,SRX18114784,SRS15617123,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.91734,,0.22049,,0.77981,,0.48624,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71869,SRR22135247,SRX18114784,SRS15617123,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,D Emergency granulopoiesis neutrophils  post infection  rep 2,GSM6704382,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,D Emergency granulopoiesis neutrophils  post infection  rep 2,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,GSM6704382,GSM6704382: D Emergency granulopoiesis neutrophils  post infection  rep 2; Danio rerio; RNA Seq,GSM6704382 r1,GSM6704382,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,D2_S14_L002_R1_001.fastq.gz,fastq,614630529.0,8159803.0,GSM6704382 r2,0:75.32,A:172330413;C:134368821;G:138082642;T:169768983;N:79670,75,,,,172330413,134368821,138082642,169768983,79670,SRX18114784,SRS15617123,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.91718,,0.22076,,0.78216,,0.48999,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71870,SRR22135248,SRX18114784,SRS15617123,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,D Emergency granulopoiesis neutrophils  post infection  rep 2,GSM6704382,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,D Emergency granulopoiesis neutrophils  post infection  rep 2,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,GSM6704382,GSM6704382: D Emergency granulopoiesis neutrophils  post infection  rep 2; Danio rerio; RNA Seq,GSM6704382 r1,GSM6704382,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,D2_S14_L003_R1_001.fastq.gz,fastq,632075043.0,8391673.0,GSM6704382 r3,0:75.32,A:177241582;C:138262538;G:141930731;T:174553877;N:86315,75,,,,177241582,138262538,141930731,174553877,86315,SRX18114784,SRS15617123,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.91775,,0.22141,,0.78125,,0.48963,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71871,SRR22135249,SRX18114784,SRS15617123,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,D Emergency granulopoiesis neutrophils  post infection  rep 2,GSM6704382,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,D Emergency granulopoiesis neutrophils  post infection  rep 2,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,GSM6704382,GSM6704382: D Emergency granulopoiesis neutrophils  post infection  rep 2; Danio rerio; RNA Seq,GSM6704382 r1,GSM6704382,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,D2_S14_L004_R1_001.fastq.gz,fastq,626788952.0,8320830.0,GSM6704382 r4,0:75.33,A:175855705;C:136981154;G:140605741;T:173263179;N:83173,75,,,,175855705,136981154,140605741,173263179,83173,SRX18114784,SRS15617123,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.91555,,0.22131,,0.78021,,0.48958,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71872,SRR22135250,SRX18114783,SRS15617122,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,D Emergency granulopoiesis neutrophils  post infection  rep 1,GSM6704381,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,D Emergency granulopoiesis neutrophils  post infection  rep 1,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,GSM6704381,GSM6704381: D Emergency granulopoiesis neutrophils  post infection  rep 1; Danio rerio; RNA Seq,GSM6704381 r1,GSM6704381,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,D1_S13_L001_R1_001.fastq.gz,fastq,600629404.0,7963900.0,GSM6704381 r1,0:75.42,A:173903456;C:125449559;G:128569714;T:172648882;N:57793,75,,,,173903456,125449559,128569714,172648882,57793,SRX18114783,SRS15617122,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.90278,,0.30767,,0.77122,,0.47302,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71873,SRR22135251,SRX18114783,SRS15617122,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,D Emergency granulopoiesis neutrophils  post infection  rep 1,GSM6704381,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,D Emergency granulopoiesis neutrophils  post infection  rep 1,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,GSM6704381,GSM6704381: D Emergency granulopoiesis neutrophils  post infection  rep 1; Danio rerio; RNA Seq,GSM6704381 r1,GSM6704381,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,D1_S13_L002_R1_001.fastq.gz,fastq,593575447.0,7870109.0,GSM6704381 r2,0:75.42,A:171856506;C:123898037;G:127183143;T:170577543;N:60218,75,,,,171856506,123898037,127183143,170577543,60218,SRX18114783,SRS15617122,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.90213,,0.30675,,0.77139,,0.49143,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71874,SRR22135252,SRX18114783,SRS15617122,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,D Emergency granulopoiesis neutrophils  post infection  rep 1,GSM6704381,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,D Emergency granulopoiesis neutrophils  post infection  rep 1,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,GSM6704381,GSM6704381: D Emergency granulopoiesis neutrophils  post infection  rep 1; Danio rerio; RNA Seq,GSM6704381 r1,GSM6704381,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,D1_S13_L003_R1_001.fastq.gz,fastq,607759183.0,8058183.0,GSM6704381 r3,0:75.42,A:175961893;C:126968252;G:130145843;T:174622136;N:61059,75,,,,175961893,126968252,130145843,174622136,61059,SRX18114783,SRS15617122,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.90286,,0.3077,,0.77536,,0.48168,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71875,SRR22135253,SRX18114783,SRS15617122,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,D Emergency granulopoiesis neutrophils  post infection  rep 1,GSM6704381,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,D Emergency granulopoiesis neutrophils  post infection  rep 1,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infection,GSM6704381,GSM6704381: D Emergency granulopoiesis neutrophils  post infection  rep 1; Danio rerio; RNA Seq,GSM6704381 r1,GSM6704381,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,D1_S13_L004_R1_001.fastq.gz,fastq,603840714.0,8006177.0,GSM6704381 r4,0:75.42,A:174992048;C:125976469;G:129096065;T:173715134;N:60998,75,,,,174992048,125976469,129096065,173715134,60998,SRX18114783,SRS15617122,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.90246,,0.30756,,0.77376,,0.49091,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71876,SRR22135254,SRX18114782,SRS15617121,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,C Emergency granulopoiesis neutrophils  before infection  rep 4,GSM6704380,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,C Emergency granulopoiesis neutrophils  before infection  rep 4,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,GSM6704380,GSM6704380: C Emergency granulopoiesis neutrophils  before infection  rep 4; Danio rerio; RNA Seq,GSM6704380 r1,GSM6704380,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,C4_S12_L001_R1_001.fastq.gz,fastq,508969256.0,6764957.0,GSM6704380 r1,0:75.24,A:141573006;C:112320231;G:115240302;T:139729984;N:105733,75,,,,141573006,112320231,115240302,139729984,105733,SRX18114782,SRS15617121,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.91769,,0.18294,,0.79022,,0.45268,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71877,SRR22135255,SRX18114782,SRS15617121,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,C Emergency granulopoiesis neutrophils  before infection  rep 4,GSM6704380,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,C Emergency granulopoiesis neutrophils  before infection  rep 4,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,GSM6704380,GSM6704380: C Emergency granulopoiesis neutrophils  before infection  rep 4; Danio rerio; RNA Seq,GSM6704380 r1,GSM6704380,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,C4_S12_L002_R1_001.fastq.gz,fastq,497898449.0,6617513.0,GSM6704380 r2,0:75.24,A:138484840;C:109817035;G:112807273;T:136689722;N:99579,75,,,,138484840,109817035,112807273,136689722,99579,SRX18114782,SRS15617121,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.91685,,0.18325,,0.79097,,0.45681,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71878,SRR22135256,SRX18114782,SRS15617121,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,C Emergency granulopoiesis neutrophils  before infection  rep 4,GSM6704380,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,C Emergency granulopoiesis neutrophils  before infection  rep 4,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,GSM6704380,GSM6704380: C Emergency granulopoiesis neutrophils  before infection  rep 4; Danio rerio; RNA Seq,GSM6704380 r1,GSM6704380,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,C4_S12_L003_R1_001.fastq.gz,fastq,507294699.0,6742347.0,GSM6704380 r3,0:75.24,A:141086540;C:111970071;G:114847428;T:139285500;N:105160,75,,,,141086540,111970071,114847428,139285500,105160,SRX18114782,SRS15617121,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.91678,,0.18312,,0.79005,,0.45106,,39,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71879,SRR22135257,SRX18114782,SRS15617121,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,C Emergency granulopoiesis neutrophils  before infection  rep 4,GSM6704380,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,C Emergency granulopoiesis neutrophils  before infection  rep 4,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,GSM6704380,GSM6704380: C Emergency granulopoiesis neutrophils  before infection  rep 4; Danio rerio; RNA Seq,GSM6704380 r1,GSM6704380,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,C4_S12_L004_R1_001.fastq.gz,fastq,506020854.0,6725110.0,GSM6704380 r4,0:75.24,A:140855644;C:111555468;G:114417168;T:139090690;N:101884,75,,,,140855644,111555468,114417168,139090690,101884,SRX18114782,SRS15617121,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.9177,,0.18523,,0.79044,,0.45269,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71880,SRR22135258,SRX18114781,SRS15617120,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,C Emergency granulopoiesis neutrophils  before infection  rep 3,GSM6704379,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,C Emergency granulopoiesis neutrophils  before infection  rep 3,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,GSM6704379,GSM6704379: C Emergency granulopoiesis neutrophils  before infection  rep 3; Danio rerio; RNA Seq,GSM6704379 r1,GSM6704379,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,C3_S11_L001_R1_001.fastq.gz,fastq,515541266.0,6855812.0,GSM6704379 r1,0:75.20,A:144554779;C:112398878;G:115543169;T:142918279;N:126161,75,,,,144554779,112398878,115543169,142918279,126161,SRX18114781,SRS15617120,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.90004,,0.21641,,0.78319,,0.4509,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71881,SRR22135259,SRX18114781,SRS15617120,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,C Emergency granulopoiesis neutrophils  before infection  rep 3,GSM6704379,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,C Emergency granulopoiesis neutrophils  before infection  rep 3,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,GSM6704379,GSM6704379: C Emergency granulopoiesis neutrophils  before infection  rep 3; Danio rerio; RNA Seq,GSM6704379 r1,GSM6704379,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,C3_S11_L002_R1_001.fastq.gz,fastq,503385097.0,6693566.0,GSM6704379 r2,0:75.20,A:141115462;C:109707827;G:112901695;T:139545873;N:114240,75,,,,141115462,109707827,112901695,139545873,114240,SRX18114781,SRS15617120,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.89994,,0.21764,,0.78439,,0.45429,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71882,SRR22135260,SRX18114781,SRS15617120,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,C Emergency granulopoiesis neutrophils  before infection  rep 3,GSM6704379,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,C Emergency granulopoiesis neutrophils  before infection  rep 3,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,GSM6704379,GSM6704379: C Emergency granulopoiesis neutrophils  before infection  rep 3; Danio rerio; RNA Seq,GSM6704379 r1,GSM6704379,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,C3_S11_L003_R1_001.fastq.gz,fastq,514809631.0,6845860.0,GSM6704379 r3,0:75.20,A:144414867;C:112234002;G:115354218;T:142684425;N:122119,75,,,,144414867,112234002,115354218,142684425,122119,SRX18114781,SRS15617120,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.90029,,0.21717,,0.78543,,0.45288,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71883,SRR22135261,SRX18114781,SRS15617120,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,C Emergency granulopoiesis neutrophils  before infection  rep 3,GSM6704379,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,C Emergency granulopoiesis neutrophils  before infection  rep 3,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,GSM6704379,GSM6704379: C Emergency granulopoiesis neutrophils  before infection  rep 3; Danio rerio; RNA Seq,GSM6704379 r1,GSM6704379,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,C3_S11_L004_R1_001.fastq.gz,fastq,511959662.0,6807750.0,GSM6704379 r4,0:75.20,A:143660849;C:111541802;G:114619614;T:142010084;N:127313,75,,,,143660849,111541802,114619614,142010084,127313,SRX18114781,SRS15617120,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.90154,,0.21666,,0.78409,,0.44479,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71884,SRR22135262,SRX18114780,SRS15617119,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,C Emergency granulopoiesis neutrophils  before infection  rep 2,GSM6704378,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,C Emergency granulopoiesis neutrophils  before infection  rep 2,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,GSM6704378,GSM6704378: C Emergency granulopoiesis neutrophils  before infection  rep 2; Danio rerio; RNA Seq,GSM6704378 r1,GSM6704378,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,C2_S10_L001_R1_001.fastq.gz,fastq,552657716.0,7351840.0,GSM6704378 r1,0:75.17,A:154321273;C:121108427;G:124253085;T:152829634;N:145297,75,,,,154321273,121108427,124253085,152829634,145297,SRX18114780,SRS15617119,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.90595,,0.21524,,0.78727,,0.44305,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71885,SRR22135263,SRX18114780,SRS15617119,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,C Emergency granulopoiesis neutrophils  before infection  rep 2,GSM6704378,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,C Emergency granulopoiesis neutrophils  before infection  rep 2,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,GSM6704378,GSM6704378: C Emergency granulopoiesis neutrophils  before infection  rep 2; Danio rerio; RNA Seq,GSM6704378 r1,GSM6704378,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,C2_S10_L002_R1_001.fastq.gz,fastq,541084407.0,7197405.0,GSM6704378 r2,0:75.18,A:151110182;C:118494427;G:121734523;T:149606835;N:138440,75,,,,151110182,118494427,121734523,149606835,138440,SRX18114780,SRS15617119,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.90451,,0.21355,,0.7864,,0.46217,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71886,SRR22135264,SRX18114780,SRS15617119,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,C Emergency granulopoiesis neutrophils  before infection  rep 2,GSM6704378,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,C Emergency granulopoiesis neutrophils  before infection  rep 2,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,GSM6704378,GSM6704378: C Emergency granulopoiesis neutrophils  before infection  rep 2; Danio rerio; RNA Seq,GSM6704378 r1,GSM6704378,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,C2_S10_L003_R1_001.fastq.gz,fastq,552243490.0,7345866.0,GSM6704378 r3,0:75.18,A:154273133;C:121031449;G:124104784;T:152689350;N:144774,75,,,,154273133,121031449,124104784,152689350,144774,SRX18114780,SRS15617119,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.90328,,0.21377,,0.78794,,0.46314,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71887,SRR22135265,SRX18114780,SRS15617119,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,C Emergency granulopoiesis neutrophils  before infection  rep 2,GSM6704378,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,C Emergency granulopoiesis neutrophils  before infection  rep 2,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,GSM6704378,GSM6704378: C Emergency granulopoiesis neutrophils  before infection  rep 2; Danio rerio; RNA Seq,GSM6704378 r1,GSM6704378,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,C2_S10_L004_R1_001.fastq.gz,fastq,550045892.0,7316300.0,GSM6704378 r4,0:75.18,A:153756888;C:120418987;G:123493369;T:152233493;N:143155,75,,,,153756888,120418987,123493369,152233493,143155,SRX18114780,SRS15617119,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.90607,,0.21521,,0.78884,,0.4602,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71888,SRR22135266,SRX18114779,SRS15617118,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,C Emergency granulopoiesis neutrophils  before infection  rep 1,GSM6704377,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,C Emergency granulopoiesis neutrophils  before infection  rep 1,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,GSM6704377,GSM6704377: C Emergency granulopoiesis neutrophils  before infection  rep 1; Danio rerio; RNA Seq,GSM6704377 r1,GSM6704377,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,C1_S9_L001_R1_001.fastq.gz,fastq,447668353.0,5946872.0,GSM6704377 r1,0:75.28,A:126591403;C:96173272;G:98995296;T:125821091;N:87291,75,,,,126591403,96173272,98995296,125821091,87291,SRX18114779,SRS15617118,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.9068,,0.19712,,0.78403,,0.44792,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71889,SRR22135267,SRX18114779,SRS15617118,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,C Emergency granulopoiesis neutrophils  before infection  rep 1,GSM6704377,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,C Emergency granulopoiesis neutrophils  before infection  rep 1,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,GSM6704377,GSM6704377: C Emergency granulopoiesis neutrophils  before infection  rep 1; Danio rerio; RNA Seq,GSM6704377 r1,GSM6704377,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,C1_S9_L002_R1_001.fastq.gz,fastq,438741991.0,5827957.0,GSM6704377 r2,0:75.28,A:124052360;C:94187980;G:97086359;T:123328717;N:86575,75,,,,124052360,94187980,97086359,123328717,86575,SRX18114779,SRS15617118,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.90575,,0.19469,,0.78372,,0.44497,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71890,SRR22135268,SRX18114779,SRS15617118,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,C Emergency granulopoiesis neutrophils  before infection  rep 1,GSM6704377,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,C Emergency granulopoiesis neutrophils  before infection  rep 1,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,GSM6704377,GSM6704377: C Emergency granulopoiesis neutrophils  before infection  rep 1; Danio rerio; RNA Seq,GSM6704377 r1,GSM6704377,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,C1_S9_L003_R1_001.fastq.gz,fastq,445278983.0,5914944.0,GSM6704377 r3,0:75.28,A:125938011;C:95660137;G:98439497;T:125152218;N:89120,75,,,,125938011,95660137,98439497,125152218,89120,SRX18114779,SRS15617118,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.90509,,0.19724,,0.78368,,0.44808,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71891,SRR22135269,SRX18114779,SRS15617118,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,C Emergency granulopoiesis neutrophils  before infection  rep 1,GSM6704377,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,C Emergency granulopoiesis neutrophils  before infection  rep 1,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:Before infection,GSM6704377,GSM6704377: C Emergency granulopoiesis neutrophils  before infection  rep 1; Danio rerio; RNA Seq,GSM6704377 r1,GSM6704377,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,C1_S9_L004_R1_001.fastq.gz,fastq,445891044.0,5922741.0,GSM6704377 r4,0:75.28,A:126199901;C:95673429;G:98452672;T:125477132;N:87910,75,,,,126199901,95673429,98452672,125477132,87910,SRX18114779,SRS15617118,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.90585,,0.19754,,0.78599,,0.44544,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71892,SRR22135270,SRX18114778,SRS15617117,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,B Steady state neutrophils  post infection  rep 4,GSM6704376,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infecton,B Steady state neutrophils  post infection  rep 4,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infecton,GSM6704376,GSM6704376: B Steady state neutrophils  post infection  rep 4; Danio rerio; RNA Seq,GSM6704376 r1,GSM6704376,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,B4_S8_L001_R1_001.fastq.gz,fastq,574532012.0,7627510.0,GSM6704376 r1,0:75.32,A:163780397;C:122304319;G:125503282;T:162857913;N:86101,75,,,,163780397,122304319,125503282,162857913,86101,SRX18114778,SRS15617117,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.90532,,0.25104,,0.80904,,0.49523,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System
71893,SRR22135271,SRX18114778,SRS15617117,SRP405741,PRJNA896643,Transcriptomic analysis of emergency granulopoiesis generated neutrophils compared to steady state control neutrophils,GSE217064,Transcriptome Analysis,Functional analysis demonstrates that neutrophils generated by emergency granulopoiesis have elevated bactericidal activity when compared to control steady state neutrophils. To determine if transcriptomic changes support these functional adaptations  we performed gene expression analysis on emergency granulopoiesis and steady state neutrophils before and post infection. Overall design: Differential gene expression analysis of RNA seq data from neutrophils generated by steady state control granulopoiesis or emergency granulopoiesis either before or post infection in biological quadruplet.,,pubmed:37672586,,B Steady state neutrophils  post infection  rep 4,GSM6704376,,tissue:Neutrophil|cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infecton,B Steady state neutrophils  post infection  rep 4,The filtered clean reads were mapped to the Danio rerio reference genome GRCz11 by HISAT2. Expression levels were measured as FPKM using the Cuffquant and Cuffnorm components of Cufflinks software. DESeq was used to analyse the DEGs between sets of two groups as a control treatment pairwise comparison. The expression log2FC was set to >1 and the FDR was set to <0.05. Assembly: GRCz11 Supplementary files format and content: Comma separated value files show FPKM  Log2FC  and adj P value of DEGs in the 'A vs C' and 'B vs D' pairwise comparisons Supplementary files format and content: Excel file shows FPKM of upregulated DEGs that were uniquely upregulated in emergency granulopoiesis neutrophils post infection and used for GO:BP analysis,Neutrophil,At 4 dpf  neutrophils from larvae undergoing steady state or emergency granulopoiesis were isolated either before infection  or at 3 hours post infection with Salmonella.,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,Tglyz:DsRED2 zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28C,cell type:Neutrophil|genotype:Tglyz:DsRED2|treatment:post infecton,GSM6704376,GSM6704376: B Steady state neutrophils  post infection  rep 4; Danio rerio; RNA Seq,GSM6704376 r1,GSM6704376,1,Larvae were homogenised in 0.25% trypsin with mechanical agitation prior to FACS isolation of 1000 neutrophils per sample. cDNA was synthesised directly from cell lysates using the SMART Seq v4 Ultra Low Input RNA kit for sequencing Takara Bio Libraries were made using the Nextera XT DNA Library Preparation Kit Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP405741,,loader:fastq load.py,B4_S8_L002_R1_001.fastq.gz,fastq,567091661.0,7528335.0,GSM6704376 r2,0:75.33,A:161676443;C:120637867;G:123939259;T:160748764;N:89328,75,,,,161676443,120637867,123939259,160748764,89328,SRX18114778,SRS15617117,SRA1532054,"Hall, FMHS, University of Auckland","Hall, FMHS, University of Auckland",1,0.9036,,0.25306,,0.81195,,0.4996,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,New Zealand,2022-11-01,Larval,Larval,Blood,Hematopoietic System