{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"cDNA\" and technology = \"celseq\"", "rows": [[25228, "SRR25685572", "SRX21410761", "SRS18649243", "SRP455780", "PRJNA1006660", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish]", "GSE241156", "Other", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "zebrafish 14dpi heart3", "GSM7717530", null, "source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi|geo loc name:missing|collection date:missing", "zebrafish 14dpi heart3", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse  danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish", "adult heart", "Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  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Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "zebrafish 14dpi heart2", "GSM7717529", null, "source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi|geo loc name:missing|collection date:missing", "zebrafish 14dpi heart2", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse  danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish", "adult heart", "Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  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Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "zebrafish 14dpi heart1", "GSM7717528", null, "source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi|geo loc name:missing|collection date:missing", "zebrafish 14dpi heart1", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse  danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish", "adult heart", "Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  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Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "zebrafish 7dpi heart3", "GSM7717527", null, "source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi|geo loc name:missing|collection date:missing", "zebrafish 7dpi heart3", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse  danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish", "adult heart", "Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell", null, "tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi", "GSM7717527", "GSM7717527: zebrafish 7dpi heart3; Danio rerio; RNA Seq", "GSM7717527 r1", "GSM7717527", "1", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  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Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "zebrafish 7dpi heart2", "GSM7717526", null, "source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi|geo loc name:missing|collection date:missing", "zebrafish 7dpi heart2", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse  danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish", "adult heart", "Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell", null, "tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi", "GSM7717526", "GSM7717526: zebrafish 7dpi heart2; Danio rerio; RNA Seq", "GSM7717526 r1", "GSM7717526", "1", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  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Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "zebrafish 7dpi heart1", "GSM7717525", null, "source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi|geo loc name:missing|collection date:missing", "zebrafish 7dpi heart1", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse  danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish", "adult heart", "Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell", null, "tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:7dpi", "GSM7717525", "GSM7717525: zebrafish 7dpi heart1; Danio rerio; RNA Seq", "GSM7717525 r1", "GSM7717525", "1", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP455780", null, "loader:fastq load.py|options:  allowEarlyFileEnd", "D17DPIZF1_R1.fq D17DPIZF1_R2.fq", "fastq fastq", 1073044507.0, 7624815.0, "GSM7717525 r1", null, "A:288576038;C:136858647;G:170330711;T:475869519;N:1409592", null, null, null, null, 288576038, 136858647, 170330711, 475869519, 1409592, "SRX21410756", "SRS18649238", "SRA1751823", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.15938, 0.70435, 0.14583, 0.08079, 0.99981, 0.87949, 0.38461, 0.57027, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25234, "SRR25685578", "SRX21410755", "SRS18649237", "SRP455780", "PRJNA1006660", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish]", "GSE241156", "Other", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "zebrafish 3dpi heart3", "GSM7717524", null, "source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi|geo loc name:missing|collection date:missing", "zebrafish 3dpi heart3", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse  danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish", "adult heart", "Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell", null, "tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi", "GSM7717524", "GSM7717524: zebrafish 3dpi heart3; Danio rerio; RNA Seq", "GSM7717524 r1", "GSM7717524", "1", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP455780", null, null, "FKHEART3_R1.fastq FKHEART3_R2.fastq", "fastq fastq", 781079621.0, 5184230.0, "GSM7717524 r1", "0:75.26 1:75.40", "A:277491111;C:118539142;G:116911958;T:268048500;N:88910", 75, 75, null, null, 277491111, 118539142, 116911958, 268048500, 88910, "SRX21410755", "SRS18649237", "SRA1751823", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.04348, 0.71869, 0.04347, 0.28823, 1.0, 0.79681, null, 0.53909, 76, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25235, "SRR25685579", "SRX21410754", "SRS18649236", "SRP455780", "PRJNA1006660", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish]", "GSE241156", "Other", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "zebrafish 3dpi heart2", "GSM7717523", null, "source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi|geo loc name:missing|collection date:missing", "zebrafish 3dpi heart2", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse  danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish", "adult heart", "Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell", null, "tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi", "GSM7717523", "GSM7717523: zebrafish 3dpi heart2; Danio rerio; RNA Seq", "GSM7717523 r1", "GSM7717523", "1", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP455780", null, null, "FKHEART2_R1.fastq FKHEART2_R2.fastq", "fastq fastq", 684820059.0, 4547520.0, "GSM7717523 r1", "0:75.21 1:75.38", "A:258487418;C:93776953;G:97187917;T:235293267;N:74504", 75, 75, null, null, 258487418, 93776953, 97187917, 235293267, 74504, "SRX21410754", "SRS18649236", "SRA1751823", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.09406, 0.79542, 0.09405, 0.0802, 1.0, 0.83029, null, 0.56367, 75, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25236, "SRR25685580", "SRX21410753", "SRS18649235", "SRP455780", "PRJNA1006660", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish]", "GSE241156", "Other", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "zebrafish 3dpi heart1", "GSM7717522", null, "source name:adult heart|tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi|geo loc name:missing|collection date:missing", "zebrafish 3dpi heart1", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Assembly: GRCm38 for mouse  danrer9 for zebrafish Supplementary files format and content: csv file containing transcript counts per gene rows and section columns Supplementary files format and content: tables of BZ genes and interspecies comparison of BZ between mouse and zebrafish", "adult heart", "Unfixed hearts were isolated and tissue was cut out and embedded in tissue freezing medium. Blocks were cryosectioned  and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell", null, "tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:3dpi", "GSM7717522", "GSM7717522: zebrafish 3dpi heart1; Danio rerio; RNA Seq", "GSM7717522 r1", "GSM7717522", "1", "Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see also: Junker et al.  2014  Cell CEL seq protocol Hashimshony et al.  Cell Reports  2012; also  see: Junker et al.  2014  Cell", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP455780", null, null, "FKHEART1_R1.fastq FKHEART1_R2.fastq", "fastq fastq", 784558404.0, 5209213.0, "GSM7717522 r1", "0:75.22 1:75.39", "A:291009319;C:102718146;G:111606154;T:279144074;N:80711", 75, 75, null, null, 291009319, 102718146, 111606154, 279144074, 80711, "SRX21410753", "SRS18649235", "SRA1751823", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.13119, 0.82035, 0.12871, 0.08445, 0.99997, 0.82785, 0.0, 0.56254, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-18", "Adult", "Adult", "Heart", "Cardiovascular System"], [25239, "SRR25723792", "SRX21447930", "SRS18684553", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 4", "GSM7728123", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 4", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728123", "GSM7728123: hmga1a mutant plate 4; Danio rerio; RNA Seq", "GSM7728123 r1", "GSM7728123", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-008_HNWVVBGX9_S7_L001_R2_001.fastq.gz HUB-DB-008_HNWVVBGX9_S7_L001_R1_001.fastq.gz", "fastq fastq", 529790530.0, 6160355.0, "GSM7728123 r1", "0:26 1:60", "A:134254092;C:100685793;G:108463112;T:186279563;N:107970", 26, 60, null, null, 134254092, 100685793, 108463112, 186279563, 107970, "SRX21447930", "SRS18684553", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11277, 0.80912, 0.10457, 0.43275, 0.99131, 0.93933, 0.67026, 0.54274, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25240, "SRR25723793", "SRX21447930", "SRS18684553", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 4", "GSM7728123", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 4", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728123", "GSM7728123: hmga1a mutant plate 4; Danio rerio; RNA Seq", "GSM7728123 r1", "GSM7728123", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-008_HNWVVBGX9_S7_L002_R1_001.fastq.gz HUB-DB-008_HNWVVBGX9_S7_L002_R2_001.fastq.gz", "fastq fastq", 611015122.0, 7104827.0, "GSM7728123 r2", "0:26 1:60", "A:152137832;C:116026517;G:127735448;T:214967198;N:148127", 26, 60, null, null, 152137832, 116026517, 127735448, 214967198, 148127, "SRX21447930", "SRS18684553", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11413, 0.81785, 0.10565, 0.44205, 0.99119, 0.93419, 0.59743, 0.53882, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25241, "SRR25723794", "SRX21447930", "SRS18684553", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 4", "GSM7728123", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 4", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728123", "GSM7728123: hmga1a mutant plate 4; Danio rerio; RNA Seq", "GSM7728123 r1", "GSM7728123", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-008_HNWVVBGX9_S7_L003_R2_001.fastq.gz HUB-DB-008_HNWVVBGX9_S7_L003_R1_001.fastq.gz", "fastq fastq", 554981822.0, 6453277.0, "GSM7728123 r3", "0:26 1:60", "A:140664360;C:105281601;G:113575873;T:195359632;N:100356", 26, 60, null, null, 140664360, 105281601, 113575873, 195359632, 100356, "SRX21447930", "SRS18684553", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11352, 0.80651, 0.10538, 0.42971, 0.99137, 0.93994, 0.65893, 0.53098, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25242, "SRR25723795", "SRX21447930", "SRS18684553", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 4", "GSM7728123", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 4", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728123", "GSM7728123: hmga1a mutant plate 4; Danio rerio; RNA Seq", "GSM7728123 r1", "GSM7728123", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-008_HNWVVBGX9_S7_L004_R2_001.fastq.gz HUB-DB-008_HNWVVBGX9_S7_L004_R1_001.fastq.gz", "fastq fastq", 459861436.0, 5347226.0, "GSM7728123 r4", "0:26 1:60", "A:115949245;C:86913961;G:95720860;T:161187969;N:89401", 26, 60, null, null, 115949245, 86913961, 95720860, 161187969, 89401, "SRX21447930", "SRS18684553", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11249, 0.81109, 0.10407, 0.43334, 0.99135, 0.94034, 0.64852, 0.53864, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25243, "SRR25723796", "SRX21447929", "SRS18684552", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 3", "GSM7728122", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 3", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728122", "GSM7728122: hmga1a mutant plate 3; Danio rerio; RNA Seq", "GSM7728122 r1", "GSM7728122", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-007_HNWVVBGX9_S6_L001_R1_001.fastq.gz HUB-DB-007_HNWVVBGX9_S6_L001_R2_001.fastq.gz", "fastq fastq", 584059454.0, 6791389.0, "GSM7728122 r1", "0:26 1:60", "A:162038298;C:107975394;G:118251259;T:195669218;N:125285", 26, 60, null, null, 162038298, 107975394, 118251259, 195669218, 125285, "SRX21447929", "SRS18684552", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.08872, 0.68673, 0.08328, 0.37858, 0.99346, 0.94945, 0.60282, 0.42608, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25244, "SRR25723797", "SRX21447929", "SRS18684552", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 3", "GSM7728122", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 3", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728122", "GSM7728122: hmga1a mutant plate 3; Danio rerio; RNA Seq", "GSM7728122 r1", "GSM7728122", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-007_HNWVVBGX9_S6_L002_R1_001.fastq.gz HUB-DB-007_HNWVVBGX9_S6_L002_R2_001.fastq.gz", "fastq fastq", 641359448.0, 7457668.0, "GSM7728122 r2", "0:26 1:60", "A:174443468;C:118438230;G:132604485;T:215721538;N:151727", 26, 60, null, null, 174443468, 118438230, 132604485, 215721538, 151727, "SRX21447929", "SRS18684552", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.09277, 0.71427, 0.08722, 0.3942, 0.99338, 0.94594, 0.56903, 0.45872, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25245, "SRR25723798", "SRX21447929", "SRS18684552", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 3", "GSM7728122", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 3", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728122", "GSM7728122: hmga1a mutant plate 3; Danio rerio; RNA Seq", "GSM7728122 r1", "GSM7728122", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-007_HNWVVBGX9_S6_L003_R1_001.fastq.gz HUB-DB-007_HNWVVBGX9_S6_L003_R2_001.fastq.gz", "fastq fastq", 609857046.0, 7091361.0, "GSM7728122 r3", "0:26 1:60", "A:169007241;C:112556048;G:123345017;T:204831635;N:117105", 26, 60, null, null, 169007241, 112556048, 123345017, 204831635, 117105, "SRX21447929", "SRS18684552", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.09058, 0.68251, 0.08521, 0.37718, 0.99332, 0.95156, 0.59403, 0.44605, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25246, "SRR25723799", "SRX21447929", "SRS18684552", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 3", "GSM7728122", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 3", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728122", "GSM7728122: hmga1a mutant plate 3; Danio rerio; RNA Seq", "GSM7728122 r1", "GSM7728122", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-007_HNWVVBGX9_S6_L004_R1_001.fastq.gz HUB-DB-007_HNWVVBGX9_S6_L004_R2_001.fastq.gz", "fastq fastq", 514759966.0, 5985581.0, "GSM7728122 r4", "0:26 1:60", "A:142060859;C:94579961;G:106100208;T:171916257;N:102681", 26, 60, null, null, 142060859, 94579961, 106100208, 171916257, 102681, "SRX21447929", "SRS18684552", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.08962, 0.7176, 0.08411, 0.39394, 0.99293, 0.95189, 0.55398, 0.46149, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25247, "SRR25723800", "SRX21447928", "SRS18684551", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "wildtype plate 3", "GSM7728121", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "wildtype plate 3", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728121", "GSM7728121: wildtype plate 3; Danio rerio; RNA Seq", "GSM7728121 r1", "GSM7728121", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-006_HNWVVBGX9_S5_L001_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L001_R2_001.fastq.gz", "fastq fastq", 929999528.0, 10813948.0, "GSM7728121 r1", "0:26 1:60", "A:240334465;C:174255952;G:184260587;T:330943403;N:205121", 26, 60, null, null, 240334465, 174255952, 184260587, 330943403, 205121, "SRX21447928", "SRS18684551", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11113, 0.87407, 0.10304, 0.43976, 0.992, 0.93034, 0.63031, 0.44624, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25248, "SRR25723801", "SRX21447928", "SRS18684551", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "wildtype plate 3", "GSM7728121", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "wildtype plate 3", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728121", "GSM7728121: wildtype plate 3; Danio rerio; RNA Seq", "GSM7728121 r1", "GSM7728121", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-006_HNWVVBGX9_S5_L002_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L002_R2_001.fastq.gz", "fastq fastq", 987824896.0, 11486336.0, "GSM7728121 r2", "0:26 1:60", "A:251121714;C:184449811;G:201317783;T:350692225;N:243363", 26, 60, null, null, 251121714, 184449811, 201317783, 350692225, 243363, "SRX21447928", "SRS18684551", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11267, 0.87874, 0.10429, 0.4457, 0.99184, 0.92498, 0.56612, 0.45489, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25249, "SRR25723802", "SRX21447928", "SRS18684551", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "wildtype plate 3", "GSM7728121", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "wildtype plate 3", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728121", "GSM7728121: wildtype plate 3; Danio rerio; RNA Seq", "GSM7728121 r1", "GSM7728121", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-006_HNWVVBGX9_S5_L003_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L003_R2_001.fastq.gz", "fastq fastq", 959933032.0, 11162012.0, "GSM7728121 r3", "0:26 1:60", "A:247983556;C:179564753;G:190342582;T:341858456;N:183685", 26, 60, null, null, 247983556, 179564753, 190342582, 341858456, 183685, "SRX21447928", "SRS18684551", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.1118, 0.87156, 0.10348, 0.43983, 0.99149, 0.93034, 0.65287, 0.44548, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25250, "SRR25723803", "SRX21447928", "SRS18684551", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "wildtype plate 3", "GSM7728121", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "wildtype plate 3", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728121", "GSM7728121: wildtype plate 3; Danio rerio; RNA Seq", "GSM7728121 r1", "GSM7728121", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-006_HNWVVBGX9_S5_L004_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L004_R2_001.fastq.gz", "fastq fastq", 798370766.0, 9283381.0, "GSM7728121 r4", "0:26 1:60", "A:205538880;C:148510556;G:161196381;T:282964175;N:160774", 26, 60, null, null, 205538880, 148510556, 161196381, 282964175, 160774, "SRX21447928", "SRS18684551", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11018, 0.87017, 0.10214, 0.43625, 0.99226, 0.93332, 0.56058, 0.44211, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25251, "SRR25723804", "SRX21447927", "SRS18684550", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "wildtype plate 2", "GSM7728120", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "wildtype plate 2", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728120", "GSM7728120: wildtype plate 2; Danio rerio; RNA Seq", "GSM7728120 r1", "GSM7728120", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-005_HNWVVBGX9_S4_L001_R1_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L001_R2_001.fastq.gz", "fastq fastq", 806178534.0, 9374169.0, "GSM7728120 r1", "0:26 1:60", "A:213590554;C:148614157;G:163804315;T:279996916;N:172592", 26, 60, null, null, 213590554, 148614157, 163804315, 279996916, 172592, "SRX21447927", "SRS18684550", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.10778, 0.79219, 0.10092, 0.39443, 0.99255, 0.93712, 0.64412, 0.39504, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25252, "SRR25723805", "SRX21447927", "SRS18684550", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "wildtype plate 2", "GSM7728120", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "wildtype plate 2", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728120", "GSM7728120: wildtype plate 2; Danio rerio; RNA Seq", "GSM7728120 r1", "GSM7728120", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-005_HNWVVBGX9_S4_L002_R1_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L002_R2_001.fastq.gz", "fastq fastq", 874594286.0, 10169701.0, "GSM7728120 r2", "0:26 1:60", "A:227213153;C:160851586;G:182364146;T:303951184;N:214217", 26, 60, null, null, 227213153, 160851586, 182364146, 303951184, 214217, "SRX21447927", "SRS18684550", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11064, 0.80317, 0.1038, 0.40093, 0.99249, 0.9332, 0.652, 0.40914, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25253, "SRR25723806", "SRX21447927", "SRS18684550", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "wildtype plate 2", "GSM7728120", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "wildtype plate 2", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728120", "GSM7728120: wildtype plate 2; Danio rerio; RNA Seq", "GSM7728120 r1", "GSM7728120", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-005_HNWVVBGX9_S4_L003_R1_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L003_R2_001.fastq.gz", "fastq fastq", 831835860.0, 9672510.0, "GSM7728120 r3", "0:26 1:60", "A:220300204;C:153061412;G:168938657;T:289375449;N:160138", 26, 60, null, null, 220300204, 153061412, 168938657, 289375449, 160138, "SRX21447927", "SRS18684550", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.10987, 0.78665, 0.10348, 0.39264, 0.99316, 0.93661, 0.66753, 0.37676, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25254, "SRR25723807", "SRX21447927", "SRS18684550", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "wildtype plate 2", "GSM7728120", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "wildtype plate 2", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728120", "GSM7728120: wildtype plate 2; Danio rerio; RNA Seq", "GSM7728120 r1", "GSM7728120", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-005_HNWVVBGX9_S4_L004_R2_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L004_R1_001.fastq.gz", "fastq fastq", 692573136.0, 8053176.0, "GSM7728120 r4", "0:26 1:60", "A:182418113;C:126757471;G:143869511;T:239393143;N:134898", 26, 60, null, null, 182418113, 126757471, 143869511, 239393143, 134898, "SRX21447927", "SRS18684550", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.10825, 0.81365, 0.10178, 0.40513, 0.99308, 0.94032, 0.67299, 0.41125, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25255, "SRR25723808", "SRX21447926", "SRS18684549", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 2", "GSM7728119", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 2", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728119", "GSM7728119: hmga1a mutant plate 2; Danio rerio; RNA Seq", "GSM7728119 r1", "GSM7728119", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-004_AHVKTGBGX7_S7_L001_R1_001.fastq.gz HUB-DB-004_AHVKTGBGX7_S7_L001_R2_001.fastq.gz", "fastq fastq", 364147736.0, 4234276.0, "GSM7728119 r1", "0:26 1:60", "A:94538754;C:69024492;G:68361658;T:132108181;N:114651", 26, 60, null, null, 94538754, 69024492, 68361658, 132108181, 114651, "SRX21447926", "SRS18684549", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11558, 0.78278, 0.10659, 0.24226, 0.9893, 0.92719, 0.58692, 0.48105, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25256, "SRR25723809", "SRX21447926", "SRS18684549", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 2", "GSM7728119", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 2", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728119", "GSM7728119: hmga1a mutant plate 2; Danio rerio; RNA Seq", "GSM7728119 r1", "GSM7728119", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-004_AHVKTGBGX7_S7_L002_R1_001.fastq.gz HUB-DB-004_AHVKTGBGX7_S7_L002_R2_001.fastq.gz", "fastq fastq", 377653262.0, 4391317.0, "GSM7728119 r2", "0:26 1:60", "A:99999342;C:71104204;G:70005970;T:136434888;N:108858", 26, 60, null, null, 99999342, 71104204, 70005970, 136434888, 108858, "SRX21447926", "SRS18684549", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11405, 0.77996, 0.10525, 0.24008, 0.98963, 0.93616, 0.60855, 0.44129, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25257, "SRR25723810", "SRX21447926", "SRS18684549", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 2", "GSM7728119", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 2", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728119", "GSM7728119: hmga1a mutant plate 2; Danio rerio; RNA Seq", "GSM7728119 r1", "GSM7728119", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-004_AHVKTGBGX7_S7_L003_R1_001.fastq.gz HUB-DB-004_AHVKTGBGX7_S7_L003_R2_001.fastq.gz", "fastq fastq", 306947588.0, 3569158.0, "GSM7728119 r3", "0:26 1:60", "A:80261116;C:58220837;G:57196503;T:111195958;N:73174", 26, 60, null, null, 80261116, 58220837, 57196503, 111195958, 73174, "SRX21447926", "SRS18684549", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11141, 0.76713, 0.10254, 0.23772, 0.98938, 0.93314, 0.62261, 0.47885, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25258, "SRR25723811", "SRX21447926", "SRS18684549", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 2", "GSM7728119", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 2", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728119", "GSM7728119: hmga1a mutant plate 2; Danio rerio; RNA Seq", "GSM7728119 r1", "GSM7728119", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-004_AHVKTGBGX7_S7_L004_R1_001.fastq.gz HUB-DB-004_AHVKTGBGX7_S7_L004_R2_001.fastq.gz", "fastq fastq", 389472414.0, 4528749.0, "GSM7728119 r4", "0:26 1:60", "A:102486709;C:73105388;G:73019179;T:140769931;N:91207", 26, 60, null, null, 102486709, 73105388, 73019179, 140769931, 91207, "SRX21447926", "SRS18684549", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11502, 0.78307, 0.10673, 0.24219, 0.98967, 0.93308, 0.64527, 0.43659, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25259, "SRR25723812", "SRX21447925", "SRS18684547", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 1", "GSM7728118", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 1", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728118", "GSM7728118: hmga1a mutant plate 1; Danio rerio; RNA Seq", "GSM7728118 r1", "GSM7728118", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-003_AHVKTGBGX7_S6_L001_R1_001.fastq.gz HUB-DB-003_AHVKTGBGX7_S6_L001_R2_001.fastq.gz", "fastq fastq", 381365624.0, 4434484.0, "GSM7728118 r1", "0:26 1:60", "A:102130758;C:71032768;G:73641442;T:134437630;N:123026", 26, 60, null, null, 102130758, 71032768, 73641442, 134437630, 123026, "SRX21447925", "SRS18684547", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.10052, 0.7243, 0.09214, 0.25633, 0.9892, 0.92985, 0.52345, 0.5112, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25260, "SRR25723813", "SRX21447925", "SRS18684547", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 1", "GSM7728118", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 1", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728118", "GSM7728118: hmga1a mutant plate 1; Danio rerio; RNA Seq", "GSM7728118 r1", "GSM7728118", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-003_AHVKTGBGX7_S6_L002_R1_001.fastq.gz HUB-DB-003_AHVKTGBGX7_S6_L002_R2_001.fastq.gz", "fastq fastq", 400525220.0, 4657270.0, "GSM7728118 r2", "0:26 1:60", "A:109307778;C:73934198;G:76916762;T:140249156;N:117326", 26, 60, null, null, 109307778, 73934198, 76916762, 140249156, 117326, "SRX21447925", "SRS18684547", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.09923, 0.71601, 0.09078, 0.25139, 0.98948, 0.93914, 0.52314, 0.5078, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25261, "SRR25723814", "SRX21447925", "SRS18684547", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 1", "GSM7728118", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 1", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728118", "GSM7728118: hmga1a mutant plate 1; Danio rerio; RNA Seq", "GSM7728118 r1", "GSM7728118", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-003_AHVKTGBGX7_S6_L003_R1_001.fastq.gz HUB-DB-003_AHVKTGBGX7_S6_L003_R2_001.fastq.gz", "fastq fastq", 341364014.0, 3969349.0, "GSM7728118 r3", "0:26 1:60", "A:91716565;C:63676514;G:65563102;T:120323617;N:84216", 26, 60, null, null, 91716565, 63676514, 65563102, 120323617, 84216, "SRX21447925", "SRS18684547", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.09826, 0.7079, 0.09008, 0.2497, 0.98918, 0.93809, 0.52649, 0.49781, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25262, "SRR25723815", "SRX21447925", "SRS18684547", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "hmga1a mutant plate 1", "GSM7728118", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "hmga1a mutant plate 1", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:hmga1a mutant|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728118", "GSM7728118: hmga1a mutant plate 1; Danio rerio; RNA Seq", "GSM7728118 r1", "GSM7728118", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-003_AHVKTGBGX7_S6_L004_R1_001.fastq.gz HUB-DB-003_AHVKTGBGX7_S6_L004_R2_001.fastq.gz", "fastq fastq", 414000732.0, 4813962.0, "GSM7728118 r4", "0:26 1:60", "A:112224009;C:76213738;G:80259829;T:145201785;N:101371", 26, 60, null, null, 112224009, 76213738, 80259829, 145201785, 101371, "SRX21447925", "SRS18684547", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.10103, 0.71981, 0.09294, 0.25413, 0.98902, 0.93669, 0.52994, 0.51172, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25263, "SRR25723816", "SRX21447924", "SRS18684548", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "wildtype plate 1", "GSM7728117", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "wildtype plate 1", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728117", "GSM7728117: wildtype plate 1; Danio rerio; RNA Seq", "GSM7728117 r1", "GSM7728117", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-001_AHVKTGBGX7_S5_L001_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L001_R2_001.fastq.gz", "fastq fastq", 471703034.0, 5484919.0, "GSM7728117 r1", "0:26 1:60", "A:125045012;C:89627491;G:85413855;T:171466861;N:149815", 26, 60, null, null, 125045012, 89627491, 85413855, 171466861, 149815, "SRX21447924", "SRS18684548", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.10906, 0.68002, 0.10212, 0.30506, 0.99101, 0.94219, 0.63738, 0.45862, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25264, "SRR25723817", "SRX21447924", "SRS18684548", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "wildtype plate 1", "GSM7728117", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "wildtype plate 1", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728117", "GSM7728117: wildtype plate 1; Danio rerio; RNA Seq", "GSM7728117 r1", "GSM7728117", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-001_AHVKTGBGX7_S5_L002_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L002_R2_001.fastq.gz", "fastq fastq", 489372938.0, 5690383.0, "GSM7728117 r2", "0:26 1:60", "A:131516821;C:92202683;G:88685608;T:176824985;N:142841", 26, 60, null, null, 131516821, 92202683, 88685608, 176824985, 142841, "SRX21447924", "SRS18684548", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.11042, 0.68086, 0.10299, 0.30411, 0.99093, 0.94856, 0.60224, 0.46578, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25265, "SRR25723818", "SRX21447924", "SRS18684548", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "wildtype plate 1", "GSM7728117", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "wildtype plate 1", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728117", "GSM7728117: wildtype plate 1; Danio rerio; RNA Seq", "GSM7728117 r1", "GSM7728117", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-001_AHVKTGBGX7_S5_L003_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L003_R2_001.fastq.gz", "fastq fastq", 407735288.0, 4741108.0, "GSM7728117 r3", "0:26 1:60", "A:108841476;C:77418215;G:73171345;T:148203998;N:100254", 26, 60, null, null, 108841476, 77418215, 73171345, 148203998, 100254, "SRX21447924", "SRS18684548", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.10882, 0.67068, 0.10177, 0.29557, 0.99151, 0.94686, 0.65762, 0.42658, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [25266, "SRR25723819", "SRX21447924", "SRS18684548", "SRP456323", "PRJNA1008049", "Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [scRNA seq]", "GSE241390", "Transcriptome Analysis", "The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.", "parent bioproject:PRJNA1006653", "pubmed:39747457", null, "wildtype plate 1", "GSM7728117", null, "source name:adult heart|tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury|geo loc name:missing|collection date:missing", "wildtype plate 1", "Based on the distribution of the log10 total reads plotted against the frequency  we introduced a cutoff at minimally 600 reads per cell to be included for further analysis which left us with a total of 1310 cells 653 wildtype and 657 hmga1a /  cells. Next  single cell data was analyzed using Seurat 81. Using the following parameters: Variable features = all genes  dimensions = 8  resolution = 0.7. This resulted in the identification of 6 clusters which were plotted in a two dimensional UMAP. Monocle2 was used to identify genes that were differentially expressed over pseudo time and organized in a self organizing map with of 8 modules. Pseudo temporal values assigned to single cells were integrated in our Seurat object and the pseudo temporal ordering was plotted on the UMAP. DAVID was used to perform GO analysis for the 8 modules. Assembly: danrer9 Supplementary files format and content: excel file containing pseudotime modules and their  genes and GO terms per module Supplementary files format and content: count tables transcriptcounts", "adult heart", "cryoinjury was performed 7 days before hearts were extracted", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "tissue:adult heart|genotype:nppa:mCitrine|genotype:wildtype|cell type:border z1 cardiomyocytes|treatment:7 days post cryoinjury", "GSM7728117", "GSM7728117: wildtype plate 1; Danio rerio; RNA Seq", "GSM7728117 r1", "GSM7728117", "1", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine expression in 384 well plates  each well containing 1 cell  containing Vapor Lock oil with CEL Seq2 barcoded primers  spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at  80oC until ready for library prep. Single cell sequencing libraries were prepared by Single Cell Discoveries Utrecht  The Netherlands using the SORT seq protocol . The CEL Seq2 protocol was used for library prep Hashimshony et al.  2016. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. In total seven 384 well plates were sequenced containing one cell per well of which three were obtained from wildtype cells and four from hmga1a mutant cells.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP456323", null, null, "HUB-DB-001_AHVKTGBGX7_S5_L004_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L004_R2_001.fastq.gz", "fastq fastq", 505539304.0, 5878364.0, "GSM7728117 r4", "0:26 1:60", "A:135189083;C:94908231;G:92431583;T:182885125;N:125282", 26, 60, null, null, 135189083, 94908231, 92431583, 182885125, 125282, "SRX21447924", "SRS18684548", "SRA1698978", "Jeroen Bakkers, Hubrecht Institute", "Jeroen Bakkers, Hubrecht Institute", 2, 0.10989, 0.68603, 0.10286, 0.30542, 0.99107, 0.94777, 0.65338, 0.42121, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2023-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [30508, "SRR27764648", "SRX23429609", "SRS20284060", "SRP486518", "PRJNA1070582", "Gene expression profile of neighboring cells of cells with unfit Wnt morphogen gradient during cell competition", "GSE254439", "Transcriptome Analysis", "Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However  developing tissues also undergo dynamic morphogenesis  which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/\u00df catenin signalling gradient  which acts as a morphogen to establish embryonic anterior posterior patterning  revealed that unfit cells with abnormal Wnt/\u00df catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/\u00df catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues  this system may support tissue robustness and disease prevention. Overall design: \u00df catCA constitutive active form of \u00df catenin expressing GFP+ cells  or \u00dfcatCA unexpressing GFP  cells from \u00df catCA mosaically introduced zebrafish early embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.", null, "pubmed:39546611", null, "Mosaic GFP control GFP min lot2", "GSM8042248", null, "source name:early embryonic cell|strain:AB|tissue:early embryonic cell|developmental stage:9 hpf loc name:missing|collection date:missing", "Mosaic GFP control GFP min lot2", "Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Assembly: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm.", "early embryonic cell", null, "Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.", null, "strain:AB|tissue:early embryonic cell|developmental stage:9 hpf", "GSM8042248", "GSM8042248: Mosaic GFP control GFP min lot2; Danio rerio; RNA Seq", "GSM8042248 r1", "GSM8042248", "1", "Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP486518", null, null, "Mosaic_GFP_control_GFP_min_lot2.fastq.gz", "fastq", 7474464.0, 207624.0, "GSM8042248 r1", "0:36", "A:1796571;C:1274347;G:1548876;T:2854637;N:33", 36, null, null, null, 1796571, 1274347, 1548876, 2854637, 33, "SRX23429609", "SRS20284060", "SRA1793856", "Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University", "Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University", 1, 0.82922, null, 0.20207, null, 0.86143, null, 0.54661, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Japan", "2024-01-29", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30509, "SRR27764649", "SRX23429608", "SRS20284059", "SRP486518", "PRJNA1070582", "Gene expression profile of neighboring cells of cells with unfit Wnt morphogen gradient during cell competition", "GSE254439", "Transcriptome Analysis", "Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However  developing tissues also undergo dynamic morphogenesis  which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/\u00df catenin signalling gradient  which acts as a morphogen to establish embryonic anterior posterior patterning  revealed that unfit cells with abnormal Wnt/\u00df catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/\u00df catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues  this system may support tissue robustness and disease prevention. Overall design: \u00df catCA constitutive active form of \u00df catenin expressing GFP+ cells  or \u00dfcatCA unexpressing GFP  cells from \u00df catCA mosaically introduced zebrafish early embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.", null, "pubmed:39546611", null, "Mosaic GFP control GFP min lot1", "GSM8042247", null, "source name:early embryonic cell|strain:AB|tissue:early embryonic cell|developmental stage:9 hpf loc name:missing|collection date:missing", "Mosaic GFP control GFP min lot1", "Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Assembly: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm.", "early embryonic cell", null, "Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.", null, "strain:AB|tissue:early embryonic cell|developmental stage:9 hpf", "GSM8042247", "GSM8042247: Mosaic GFP control GFP min lot1; Danio rerio; RNA Seq", "GSM8042247 r1", "GSM8042247", "1", "Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP486518", null, null, "Mosaic_GFP_control_GFP_min_lot1.fastq.gz", "fastq", 8256240.0, 229340.0, "GSM8042247 r1", "0:36", "A:1947003;C:1345938;G:1692065;T:3271133;N:101", 36, null, null, null, 1947003, 1345938, 1692065, 3271133, 101, "SRX23429608", "SRS20284059", "SRA1793856", "Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University", "Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University", 1, 0.83305, null, 0.17754, null, 0.8619, null, 0.61474, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Japan", "2024-01-29", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30510, "SRR27764650", "SRX23429607", "SRS20284058", "SRP486518", "PRJNA1070582", "Gene expression profile of neighboring cells of cells with unfit Wnt morphogen gradient during cell competition", "GSE254439", "Transcriptome Analysis", "Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However  developing tissues also undergo dynamic morphogenesis  which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/\u00df catenin signalling gradient  which acts as a morphogen to establish embryonic anterior posterior patterning  revealed that unfit cells with abnormal Wnt/\u00df catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/\u00df catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues  this system may support tissue robustness and disease prevention. Overall design: \u00df catCA constitutive active form of \u00df catenin expressing GFP+ cells  or \u00dfcatCA unexpressing GFP  cells from \u00df catCA mosaically introduced zebrafish early embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.", null, "pubmed:39546611", null, "Mosaic beta catCA GFP min lot2", "GSM8042246", null, "source name:early embryonic cell|strain:AB|tissue:early embryonic cell|developmental stage:9 hpf loc name:missing|collection date:missing", "Mosaic beta catCA GFP min lot2", "Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Assembly: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm.", "early embryonic cell", null, "Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.", null, "strain:AB|tissue:early embryonic cell|developmental stage:9 hpf", "GSM8042246", "GSM8042246: Mosaic beta catCA GFP min lot2; Danio rerio; RNA Seq", "GSM8042246 r1", "GSM8042246", "1", "Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP486518", null, null, "Mosaic_beta-catCA_GFP_min_lot2.fastq.gz", "fastq", 856836.0, 23801.0, "GSM8042246 r1", "0:36", "A:217589;C:147419;G:175612;T:316201;N:15", 36, null, null, null, 217589, 147419, 175612, 316201, 15, "SRX23429607", "SRS20284058", "SRA1793856", "Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University", "Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University", 1, 0.82481, null, 0.28434, null, 0.95371, null, 0.61551, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Japan", "2024-01-29", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30511, "SRR27764651", "SRX23429606", "SRS20284057", "SRP486518", "PRJNA1070582", "Gene expression profile of neighboring cells of cells with unfit Wnt morphogen gradient during cell competition", "GSE254439", "Transcriptome Analysis", "Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However  developing tissues also undergo dynamic morphogenesis  which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/\u00df catenin signalling gradient  which acts as a morphogen to establish embryonic anterior posterior patterning  revealed that unfit cells with abnormal Wnt/\u00df catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/\u00df catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues  this system may support tissue robustness and disease prevention. Overall design: \u00df catCA constitutive active form of \u00df catenin expressing GFP+ cells  or \u00dfcatCA unexpressing GFP  cells from \u00df catCA mosaically introduced zebrafish early embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.", null, "pubmed:39546611", null, "Mosaic beta catCA GFP min lot1", "GSM8042245", null, "source name:early embryonic cell|strain:AB|tissue:early embryonic cell|developmental stage:9 hpf loc name:missing|collection date:missing", "Mosaic beta catCA GFP min lot1", "Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Assembly: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm.", "early embryonic cell", null, "Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.", null, "strain:AB|tissue:early embryonic cell|developmental stage:9 hpf", "GSM8042245", "GSM8042245: Mosaic beta catCA GFP min lot1; Danio rerio; RNA Seq", "GSM8042245 r1", "GSM8042245", "1", "Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP486518", null, null, "Mosaic_beta-catCA_GFP_min_lot1.fastq.gz", "fastq", 7181388.0, 199483.0, "GSM8042245 r1", "0:36", "A:1744919;C:1207643;G:1456829;T:2771919;N:78", 36, null, null, null, 1744919, 1207643, 1456829, 2771919, 78, "SRX23429606", "SRS20284057", "SRA1793856", "Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University", "Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University", 1, 0.83629, null, 0.16823, null, 0.84774, null, 0.64548, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Japan", "2024-01-29", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33075, "SRR29654109", "SRX25158199", "SRS21848821", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3", "GSM8369980", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100", "GSM8369980", "GSM8369980: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3; Danio rerio; RNA Seq", "GSM8369980 r1", "GSM8369980", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_AMD_-016_cbc.fastq.gz", "fastq", 347162880.0, 5786048.0, "GSM8369980 r1", "0:60", "A:122562825;C:62219285;G:75539895;T:86775172;N:65703", 60, null, null, null, 122562825, 62219285, 75539895, 86775172, 65703, "SRX25158199", "SRS21848821", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33076, "SRR29654110", "SRX25158199", "SRS21848821", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3", "GSM8369980", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100", "GSM8369980", "GSM8369980: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3; Danio rerio; RNA Seq", "GSM8369980 r1", "GSM8369980", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_AMD_-016_cbc.fastq.gz", "fastq", 340954260.0, 5682571.0, "GSM8369980 r2", "0:60", "A:120149623;C:60854408;G:75192893;T:84703966;N:53370", 60, null, null, null, 120149623, 60854408, 75192893, 84703966, 53370, "SRX25158199", "SRS21848821", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33077, "SRR29654111", "SRX25158199", "SRS21848821", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3", "GSM8369980", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100", "GSM8369980", "GSM8369980: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3; Danio rerio; RNA Seq", "GSM8369980 r1", "GSM8369980", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_AMD_-016_cbc.fastq.gz", "fastq", 351749160.0, 5862486.0, "GSM8369980 r3", "0:60", "A:124352905;C:63078724;G:76291828;T:87988386;N:37317", 60, null, null, null, 124352905, 63078724, 76291828, 87988386, 37317, "SRX25158199", "SRS21848821", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33078, "SRR29654112", "SRX25158199", "SRS21848821", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3", "GSM8369980", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100", "GSM8369980", "GSM8369980: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3; Danio rerio; RNA Seq", "GSM8369980 r1", "GSM8369980", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_AMD_-016_cbc.fastq.gz", "fastq", 345225720.0, 5753762.0, "GSM8369980 r4", "0:60", "A:121803902;C:61651407;G:75900430;T:85843789;N:26192", 60, null, null, null, 121803902, 61651407, 75900430, 85843789, 26192, "SRX25158199", "SRS21848821", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33079, "SRR29654113", "SRX25158198", "SRS21848820", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2", "GSM8369979", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100", "GSM8369979", "GSM8369979: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2; Danio rerio; RNA Seq", "GSM8369979 r1", "GSM8369979", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_AMD_-015_cbc.fastq.gz", "fastq", 159497640.0, 2658294.0, "GSM8369979 r1", "0:60", "A:55569742;C:28678683;G:33264744;T:41953354;N:31117", 60, null, null, null, 55569742, 28678683, 33264744, 41953354, 31117, "SRX25158198", "SRS21848820", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33080, "SRR29654114", "SRX25158198", "SRS21848820", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2", "GSM8369979", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100", "GSM8369979", "GSM8369979: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2; Danio rerio; RNA Seq", "GSM8369979 r1", "GSM8369979", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_AMD_-015_cbc.fastq.gz", "fastq", 156549240.0, 2609154.0, "GSM8369979 r2", "0:60", "A:54428858;C:28027289;G:33149650;T:40918247;N:25196", 60, null, null, null, 54428858, 28027289, 33149650, 40918247, 25196, "SRX25158198", "SRS21848820", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33081, "SRR29654115", "SRX25158198", "SRS21848820", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2", "GSM8369979", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100", "GSM8369979", "GSM8369979: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2; Danio rerio; RNA Seq", "GSM8369979 r1", "GSM8369979", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_AMD_-015_cbc.fastq.gz", "fastq", 161735280.0, 2695588.0, "GSM8369979 r3", "0:60", "A:56425187;C:29084972;G:33637112;T:42570603;N:17406", 60, null, null, null, 56425187, 29084972, 33637112, 42570603, 17406, "SRX25158198", "SRS21848820", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33082, "SRR29654116", "SRX25158198", "SRS21848820", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2", "GSM8369979", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100", "GSM8369979", "GSM8369979: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2; Danio rerio; RNA Seq", "GSM8369979 r1", "GSM8369979", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_AMD_-015_cbc.fastq.gz", "fastq", 158621520.0, 2643692.0, "GSM8369979 r4", "0:60", "A:55213721;C:28430013;G:33462307;T:41503213;N:12266", 60, null, null, null, 55213721, 28430013, 33462307, 41503213, 12266, "SRX25158198", "SRS21848820", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33083, "SRR29654117", "SRX25158197", "SRS21848819", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1", "GSM8369978", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100", "GSM8369978", "GSM8369978: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1; Danio rerio; RNA Seq", "GSM8369978 r1", "GSM8369978", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_AMD_-011_cbc.fastq.gz", "fastq", 44363040.0, 739384.0, "GSM8369978 r1", "0:60", "A:17756825;C:7540147;G:9311367;T:9746444;N:8257", 60, null, null, null, 17756825, 7540147, 9311367, 9746444, 8257, "SRX25158197", "SRS21848819", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33084, "SRR29654118", "SRX25158197", "SRS21848819", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1", "GSM8369978", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100", "GSM8369978", "GSM8369978: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1; Danio rerio; RNA Seq", "GSM8369978 r1", "GSM8369978", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_AMD_-011_cbc.fastq.gz", "fastq", 43450800.0, 724180.0, "GSM8369978 r2", "0:60", "A:17376442;C:7355139;G:9244019;T:9468455;N:6745", 60, null, null, null, 17376442, 7355139, 9244019, 9468455, 6745, "SRX25158197", "SRS21848819", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33085, "SRR29654119", "SRX25158197", "SRS21848819", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1", "GSM8369978", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100", "GSM8369978", "GSM8369978: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1; Danio rerio; RNA Seq", "GSM8369978 r1", "GSM8369978", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_AMD_-011_cbc.fastq.gz", "fastq", 44795880.0, 746598.0, "GSM8369978 r3", "0:60", "A:17988707;C:7600964;G:9362568;T:9839285;N:4356", 60, null, null, null, 17988707, 7600964, 9362568, 9839285, 4356, "SRX25158197", "SRS21848819", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33086, "SRR29654120", "SRX25158197", "SRS21848819", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1", "GSM8369978", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100", "GSM8369978", "GSM8369978: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1; Danio rerio; RNA Seq", "GSM8369978 r1", "GSM8369978", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_AMD_-011_cbc.fastq.gz", "fastq", 44060940.0, 734349.0, "GSM8369978 r4", "0:60", "A:17608648;C:7492643;G:9327676;T:9628642;N:3331", 60, null, null, null, 17608648, 7492643, 9327676, 9628642, 3331, "SRX25158197", "SRS21848819", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33087, "SRR29654121", "SRX25158196", "SRS21848818", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  AMD3100  biol rep 3", "GSM8369977", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  AMD3100  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100", "GSM8369977", "GSM8369977: Neutrophils mpx+  uninjured  AMD3100  biol rep 3; Danio rerio; RNA Seq", "GSM8369977 r1", "GSM8369977", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_AMD_-014_cbc.fastq.gz", "fastq", 115048140.0, 1917469.0, "GSM8369977 r1", "0:60", "A:41373215;C:21759509;G:21832537;T:30061744;N:21135", 60, null, null, null, 41373215, 21759509, 21832537, 30061744, 21135, "SRX25158196", "SRS21848818", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33088, "SRR29654122", "SRX25158196", "SRS21848818", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  AMD3100  biol rep 3", "GSM8369977", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  AMD3100  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100", "GSM8369977", "GSM8369977: Neutrophils mpx+  uninjured  AMD3100  biol rep 3; Danio rerio; RNA Seq", "GSM8369977 r1", "GSM8369977", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_AMD_-014_cbc.fastq.gz", "fastq", 112845060.0, 1880751.0, "GSM8369977 r2", "0:60", "A:40482360;C:21287713;G:21750928;T:29306465;N:17594", 60, null, null, null, 40482360, 21287713, 21750928, 29306465, 17594, "SRX25158196", "SRS21848818", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33089, "SRR29654123", "SRX25158196", "SRS21848818", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  AMD3100  biol rep 3", "GSM8369977", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  AMD3100  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100", "GSM8369977", "GSM8369977: Neutrophils mpx+  uninjured  AMD3100  biol rep 3; Danio rerio; RNA Seq", "GSM8369977 r1", "GSM8369977", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_AMD_-014_cbc.fastq.gz", "fastq", 116696580.0, 1944943.0, "GSM8369977 r3", "0:60", "A:42022776;C:22106040;G:22075778;T:30479513;N:12473", 60, null, null, null, 42022776, 22106040, 22075778, 30479513, 12473, "SRX25158196", "SRS21848818", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33090, "SRR29654124", "SRX25158196", "SRS21848818", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  AMD3100  biol rep 3", "GSM8369977", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  AMD3100  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100", "GSM8369977", "GSM8369977: Neutrophils mpx+  uninjured  AMD3100  biol rep 3; Danio rerio; RNA Seq", "GSM8369977 r1", "GSM8369977", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_AMD_-014_cbc.fastq.gz", "fastq", 114334980.0, 1905583.0, "GSM8369977 r4", "0:60", "A:41132105;C:21578779;G:21934073;T:29681512;N:8511", 60, null, null, null, 41132105, 21578779, 21934073, 29681512, 8511, "SRX25158196", "SRS21848818", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33091, "SRR29654125", "SRX25158195", "SRS21848817", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  AMD3100  biol rep 2", "GSM8369976", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  AMD3100  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100", "GSM8369976", "GSM8369976: Neutrophils mpx+  uninjured  AMD3100  biol rep 2; Danio rerio; RNA Seq", "GSM8369976 r1", "GSM8369976", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_AMD_-013_cbc.fastq.gz", "fastq", 354085380.0, 5901423.0, "GSM8369976 r1", "0:60", "A:124800871;C:65627966;G:72434440;T:91152029;N:70074", 60, null, null, null, 124800871, 65627966, 72434440, 91152029, 70074, "SRX25158195", "SRS21848817", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33092, "SRR29654126", "SRX25158195", "SRS21848817", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  AMD3100  biol rep 2", "GSM8369976", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  AMD3100  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100", "GSM8369976", "GSM8369976: Neutrophils mpx+  uninjured  AMD3100  biol rep 2; Danio rerio; RNA Seq", "GSM8369976 r1", "GSM8369976", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_AMD_-013_cbc.fastq.gz", "fastq", 347250360.0, 5787506.0, "GSM8369976 r2", "0:60", "A:122147080;C:64042522;G:72135325;T:88869927;N:55506", 60, null, null, null, 122147080, 64042522, 72135325, 88869927, 55506, "SRX25158195", "SRS21848817", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33093, "SRR29654127", "SRX25158195", "SRS21848817", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  AMD3100  biol rep 2", "GSM8369976", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  AMD3100  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100", "GSM8369976", "GSM8369976: Neutrophils mpx+  uninjured  AMD3100  biol rep 2; Danio rerio; RNA Seq", "GSM8369976 r1", "GSM8369976", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_AMD_-013_cbc.fastq.gz", "fastq", 358862580.0, 5981043.0, "GSM8369976 r3", "0:60", "A:126636264;C:66527902;G:73214426;T:92445348;N:38640", 60, null, null, null, 126636264, 66527902, 73214426, 92445348, 38640, "SRX25158195", "SRS21848817", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33094, "SRR29654128", "SRX25158195", "SRS21848817", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  AMD3100  biol rep 2", "GSM8369976", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  AMD3100  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100", "GSM8369976", "GSM8369976: Neutrophils mpx+  uninjured  AMD3100  biol rep 2; Danio rerio; RNA Seq", "GSM8369976 r1", "GSM8369976", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_AMD_-013_cbc.fastq.gz", "fastq", 351843120.0, 5864052.0, "GSM8369976 r4", "0:60", "A:123921807;C:64956560;G:72828989;T:90107944;N:27820", 60, null, null, null, 123921807, 64956560, 72828989, 90107944, 27820, "SRX25158195", "SRS21848817", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33095, "SRR29654129", "SRX25158194", "SRS21848816", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  AMD3100  biol rep 1", "GSM8369975", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  AMD3100  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100", "GSM8369975", "GSM8369975: Neutrophils mpx+  uninjured  AMD3100  biol rep 1; Danio rerio; RNA Seq", "GSM8369975 r1", "GSM8369975", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_AMD_-010_cbc.fastq.gz", "fastq", 100732380.0, 1678873.0, "GSM8369975 r1", "0:60", "A:37215898;C:18610797;G:18111317;T:26774380;N:19988", 60, null, null, null, 37215898, 18610797, 18111317, 26774380, 19988, "SRX25158194", "SRS21848816", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33096, "SRR29654130", "SRX25158194", "SRS21848816", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  AMD3100  biol rep 1", "GSM8369975", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  AMD3100  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100", "GSM8369975", "GSM8369975: Neutrophils mpx+  uninjured  AMD3100  biol rep 1; Danio rerio; RNA Seq", "GSM8369975 r1", "GSM8369975", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_AMD_-010_cbc.fastq.gz", "fastq", 98830860.0, 1647181.0, "GSM8369975 r2", "0:60", "A:36388012;C:18195984;G:18122717;T:26108692;N:15455", 60, null, null, null, 36388012, 18195984, 18122717, 26108692, 15455, "SRX25158194", "SRS21848816", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33097, "SRR29654131", "SRX25158194", "SRS21848816", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  AMD3100  biol rep 1", "GSM8369975", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  AMD3100  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100", "GSM8369975", "GSM8369975: Neutrophils mpx+  uninjured  AMD3100  biol rep 1; Danio rerio; RNA Seq", "GSM8369975 r1", "GSM8369975", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_AMD_-010_cbc.fastq.gz", "fastq", 102277560.0, 1704626.0, "GSM8369975 r3", "0:60", "A:37811843;C:18928051;G:18347174;T:27179477;N:11015", 60, null, null, null, 37811843, 18928051, 18347174, 27179477, 11015, "SRX25158194", "SRS21848816", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33098, "SRR29654132", "SRX25158194", "SRS21848816", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  AMD3100  biol rep 1", "GSM8369975", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  AMD3100  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100", "GSM8369975", "GSM8369975: Neutrophils mpx+  uninjured  AMD3100  biol rep 1; Danio rerio; RNA Seq", "GSM8369975 r1", "GSM8369975", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_AMD_-010_cbc.fastq.gz", "fastq", 100371840.0, 1672864.0, "GSM8369975 r4", "0:60", "A:37032383;C:18500721;G:18308236;T:26522753;N:7747", 60, null, null, null, 37032383, 18500721, 18308236, 26522753, 7747, "SRX25158194", "SRS21848816", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33099, "SRR29654133", "SRX25158193", "SRS21848815", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3", "GSM8369974", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO", "GSM8369974", "GSM8369974: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3; Danio rerio; RNA Seq", "GSM8369974 r1", "GSM8369974", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_DMSO_-008_cbc.fastq.gz", "fastq", 161717520.0, 2695292.0, "GSM8369974 r1", "0:60", "A:58227035;C:29120167;G:33153372;T:41186362;N:30584", 60, null, null, null, 58227035, 29120167, 33153372, 41186362, 30584, "SRX25158193", "SRS21848815", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33100, "SRR29654134", "SRX25158193", "SRS21848815", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3", "GSM8369974", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO", "GSM8369974", "GSM8369974: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3; Danio rerio; RNA Seq", "GSM8369974 r1", "GSM8369974", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_DMSO_-008_cbc.fastq.gz", "fastq", 158810460.0, 2646841.0, "GSM8369974 r2", "0:60", "A:57059029;C:28475827;G:33090143;T:40160441;N:25020", 60, null, null, null, 57059029, 28475827, 33090143, 40160441, 25020, "SRX25158193", "SRS21848815", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33101, "SRR29654135", "SRX25158193", "SRS21848815", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3", "GSM8369974", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO", "GSM8369974", "GSM8369974: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3; Danio rerio; RNA Seq", "GSM8369974 r1", "GSM8369974", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_DMSO_-008_cbc.fastq.gz", "fastq", 164136600.0, 2735610.0, "GSM8369974 r3", "0:60", "A:59164760;C:29564845;G:33567677;T:41822336;N:16982", 60, null, null, null, 59164760, 29564845, 33567677, 41822336, 16982, "SRX25158193", "SRS21848815", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33102, "SRR29654136", "SRX25158193", "SRS21848815", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3", "GSM8369974", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO", "GSM8369974", "GSM8369974: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3; Danio rerio; RNA Seq", "GSM8369974 r1", "GSM8369974", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_DMSO_-008_cbc.fastq.gz", "fastq", 160939740.0, 2682329.0, "GSM8369974 r4", "0:60", "A:57905646;C:28872433;G:33402085;T:40746636;N:12940", 60, null, null, null, 57905646, 28872433, 33402085, 40746636, 12940, "SRX25158193", "SRS21848815", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33103, "SRR29654137", "SRX25158192", "SRS21848814", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2", "GSM8369973", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO", "GSM8369973", "GSM8369973: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2; Danio rerio; RNA Seq", "GSM8369973 r1", "GSM8369973", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_DMSO_-005_cbc.fastq.gz", "fastq", 294896760.0, 4914946.0, "GSM8369973 r1", "0:60", "A:113302890;C:53832811;G:54274745;T:73429183;N:57131", 60, null, null, null, 113302890, 53832811, 54274745, 73429183, 57131, "SRX25158192", "SRS21848814", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33104, "SRR29654138", "SRX25158192", "SRS21848814", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2", "GSM8369973", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO", "GSM8369973", "GSM8369973: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2; Danio rerio; RNA Seq", "GSM8369973 r1", "GSM8369973", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_DMSO_-005_cbc.fastq.gz", "fastq", 289658820.0, 4827647.0, "GSM8369973 r2", "0:60", "A:111138289;C:52646716;G:54190664;T:71637241;N:45910", 60, null, null, null, 111138289, 52646716, 54190664, 71637241, 45910, "SRX25158192", "SRS21848814", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33105, "SRR29654139", "SRX25158192", "SRS21848814", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2", "GSM8369973", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO", "GSM8369973", "GSM8369973: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2; Danio rerio; RNA Seq", "GSM8369973 r1", "GSM8369973", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_DMSO_-005_cbc.fastq.gz", "fastq", 299290800.0, 4988180.0, "GSM8369973 r3", "0:60", "A:115247052;C:54662821;G:54854607;T:74494831;N:31489", 60, null, null, null, 115247052, 54662821, 54854607, 74494831, 31489, "SRX25158192", "SRS21848814", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33106, "SRR29654140", "SRX25158192", "SRS21848814", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2", "GSM8369973", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO", "GSM8369973", "GSM8369973: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2; Danio rerio; RNA Seq", "GSM8369973 r1", "GSM8369973", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_DMSO_-005_cbc.fastq.gz", "fastq", 294091920.0, 4901532.0, "GSM8369973 r4", "0:60", "A:113032051;C:53520496;G:54754695;T:72762244;N:22434", 60, null, null, null, 113032051, 53520496, 54754695, 72762244, 22434, "SRX25158192", "SRS21848814", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33107, "SRR29654141", "SRX25158191", "SRS21848813", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1", "GSM8369972", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO", "GSM8369972", "GSM8369972: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1; Danio rerio; RNA Seq", "GSM8369972 r1", "GSM8369972", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_DMSO_-004_cbc.fastq.gz", "fastq", 79542600.0, 1325710.0, "GSM8369972 r1", "0:60", "A:29052800;C:15106261;G:15344010;T:20023888;N:15641", 60, null, null, null, 29052800, 15106261, 15344010, 20023888, 15641, "SRX25158191", "SRS21848813", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33108, "SRR29654142", "SRX25158191", "SRS21848813", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1", "GSM8369972", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO", "GSM8369972", "GSM8369972: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1; Danio rerio; RNA Seq", "GSM8369972 r1", "GSM8369972", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_DMSO_-004_cbc.fastq.gz", "fastq", 78150840.0, 1302514.0, "GSM8369972 r2", "0:60", "A:28490299;C:14795977;G:15298357;T:19554765;N:11442", 60, null, null, null, 28490299, 14795977, 15298357, 19554765, 11442, "SRX25158191", "SRS21848813", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33109, "SRR29654143", "SRX25158191", "SRS21848813", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1", "GSM8369972", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO", "GSM8369972", "GSM8369972: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1; Danio rerio; RNA Seq", "GSM8369972 r1", "GSM8369972", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_DMSO_-004_cbc.fastq.gz", "fastq", 80719140.0, 1345319.0, "GSM8369972 r3", "0:60", "A:29548150;C:15350378;G:15486892;T:20325654;N:8066", 60, null, null, null, 29548150, 15350378, 15486892, 20325654, 8066, "SRX25158191", "SRS21848813", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33110, "SRR29654144", "SRX25158191", "SRS21848813", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1", "GSM8369972", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO", "GSM8369972", "GSM8369972: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1; Danio rerio; RNA Seq", "GSM8369972 r1", "GSM8369972", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_DMSO_-004_cbc.fastq.gz", "fastq", 79070760.0, 1317846.0, "GSM8369972 r4", "0:60", "A:28874779;C:14986197;G:15407453;T:19795922;N:6409", 60, null, null, null, 28874779, 14986197, 15407453, 19795922, 6409, "SRX25158191", "SRS21848813", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33111, "SRR29654145", "SRX25158190", "SRS21848812", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  DMSO  biol rep 3", "GSM8369971", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  DMSO  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO", "GSM8369971", "GSM8369971: Neutrophils mpx+  uninjured  DMSO  biol rep 3; Danio rerio; RNA Seq", "GSM8369971 r1", "GSM8369971", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_DMSO_-009_cbc.fastq.gz", "fastq", 182391600.0, 3039860.0, "GSM8369971 r1", "0:60", "A:65842196;C:33929963;G:37226765;T:45358269;N:34407", 60, null, null, null, 65842196, 33929963, 37226765, 45358269, 34407, "SRX25158190", "SRS21848812", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33112, "SRR29654146", "SRX25158190", "SRS21848812", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  DMSO  biol rep 3", "GSM8369971", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  DMSO  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO", "GSM8369971", "GSM8369971: Neutrophils mpx+  uninjured  DMSO  biol rep 3; Danio rerio; RNA Seq", "GSM8369971 r1", "GSM8369971", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_DMSO_-009_cbc.fastq.gz", "fastq", 179081640.0, 2984694.0, "GSM8369971 r2", "0:60", "A:64544585;C:33163305;G:37078756;T:44266486;N:28508", 60, null, null, null, 64544585, 33163305, 37078756, 44266486, 28508, "SRX25158190", "SRS21848812", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33113, "SRR29654147", "SRX25158190", "SRS21848812", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  DMSO  biol rep 3", "GSM8369971", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  DMSO  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO", "GSM8369971", "GSM8369971: Neutrophils mpx+  uninjured  DMSO  biol rep 3; Danio rerio; RNA Seq", "GSM8369971 r1", "GSM8369971", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_DMSO_-009_cbc.fastq.gz", "fastq", 185068740.0, 3084479.0, "GSM8369971 r3", "0:60", "A:66919946;C:34450944;G:37652300;T:46025841;N:19709", 60, null, null, null, 66919946, 34450944, 37652300, 46025841, 19709, "SRX25158190", "SRS21848812", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33114, "SRR29654148", "SRX25158190", "SRS21848812", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  DMSO  biol rep 3", "GSM8369971", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  DMSO  biol rep 3", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO", "GSM8369971", "GSM8369971: Neutrophils mpx+  uninjured  DMSO  biol rep 3; Danio rerio; RNA Seq", "GSM8369971 r1", "GSM8369971", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_DMSO_-009_cbc.fastq.gz", "fastq", 181507740.0, 3025129.0, "GSM8369971 r4", "0:60", "A:65513514;C:33675079;G:37432606;T:44872485;N:14056", 60, null, null, null, 65513514, 33675079, 37432606, 44872485, 14056, "SRX25158190", "SRS21848812", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33115, "SRR29654149", "SRX25158189", "SRS21848811", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  DMSO  biol rep 2", "GSM8369970", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  DMSO  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO", "GSM8369970", "GSM8369970: Neutrophils mpx+  uninjured  DMSO  biol rep 2; Danio rerio; RNA Seq", "GSM8369970 r1", "GSM8369970", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_DMSO_-006_cbc.fastq.gz", "fastq", 45794760.0, 763246.0, "GSM8369970 r1", "0:60", "A:16928569;C:8492491;G:9006326;T:11358172;N:9202", 60, null, null, null, 16928569, 8492491, 9006326, 11358172, 9202, "SRX25158189", "SRS21848811", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33116, "SRR29654150", "SRX25158189", "SRS21848811", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  DMSO  biol rep 2", "GSM8369970", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  DMSO  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO", "GSM8369970", "GSM8369970: Neutrophils mpx+  uninjured  DMSO  biol rep 2; Danio rerio; RNA Seq", "GSM8369970 r1", "GSM8369970", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_DMSO_-006_cbc.fastq.gz", "fastq", 45009960.0, 750166.0, "GSM8369970 r2", "0:60", "A:16608407;C:8309766;G:8990622;T:11094414;N:6751", 60, null, null, null, 16608407, 8309766, 8990622, 11094414, 6751, "SRX25158189", "SRS21848811", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33117, "SRR29654151", "SRX25158189", "SRS21848811", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  DMSO  biol rep 2", "GSM8369970", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  DMSO  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO", "GSM8369970", "GSM8369970: Neutrophils mpx+  uninjured  DMSO  biol rep 2; Danio rerio; RNA Seq", "GSM8369970 r1", "GSM8369970", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_DMSO_-006_cbc.fastq.gz", "fastq", 46565880.0, 776098.0, "GSM8369970 r3", "0:60", "A:17217451;C:8640544;G:9146095;T:11557146;N:4644", 60, null, null, null, 17217451, 8640544, 9146095, 11557146, 4644, "SRX25158189", "SRS21848811", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33118, "SRR29654152", "SRX25158189", "SRS21848811", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  DMSO  biol rep 2", "GSM8369970", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  DMSO  biol rep 2", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO", "GSM8369970", "GSM8369970: Neutrophils mpx+  uninjured  DMSO  biol rep 2; Danio rerio; RNA Seq", "GSM8369970 r1", "GSM8369970", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_DMSO_-006_cbc.fastq.gz", "fastq", 45624660.0, 760411.0, "GSM8369970 r4", "0:60", "A:16852187;C:8431444;G:9090234;T:11246907;N:3888", 60, null, null, null, 16852187, 8431444, 9090234, 11246907, 3888, "SRX25158189", "SRS21848811", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33119, "SRR29654153", "SRX25158188", "SRS21848810", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  DMSO  biol rep 1", "GSM8369969", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  DMSO  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO", "GSM8369969", "GSM8369969: Neutrophils mpx+  uninjured  DMSO  biol rep 1; Danio rerio; RNA Seq", "GSM8369969 r1", "GSM8369969", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_DMSO_-003_cbc.fastq.gz", "fastq", 55867380.0, 931123.0, "GSM8369969 r1", "0:60", "A:20680346;C:10254613;G:10895370;T:14026951;N:10100", 60, null, null, null, 20680346, 10254613, 10895370, 14026951, 10100, "SRX25158188", "SRS21848810", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33120, "SRR29654154", "SRX25158188", "SRS21848810", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  DMSO  biol rep 1", "GSM8369969", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  DMSO  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO", "GSM8369969", "GSM8369969: Neutrophils mpx+  uninjured  DMSO  biol rep 1; Danio rerio; RNA Seq", "GSM8369969 r1", "GSM8369969", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_DMSO_-003_cbc.fastq.gz", "fastq", 54889080.0, 914818.0, "GSM8369969 r2", "0:60", "A:20264110;C:10026239;G:10861715;T:13728039;N:8977", 60, null, null, null, 20264110, 10026239, 10861715, 13728039, 8977, "SRX25158188", "SRS21848810", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33121, "SRR29654155", "SRX25158188", "SRS21848810", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  DMSO  biol rep 1", "GSM8369969", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  DMSO  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO", "GSM8369969", "GSM8369969: Neutrophils mpx+  uninjured  DMSO  biol rep 1; Danio rerio; RNA Seq", "GSM8369969 r1", "GSM8369969", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_DMSO_-003_cbc.fastq.gz", "fastq", 56764440.0, 946074.0, "GSM8369969 r3", "0:60", "A:21036899;C:10416984;G:11027830;T:14275499;N:7228", 60, null, null, null, 21036899, 10416984, 11027830, 14275499, 7228, "SRX25158188", "SRS21848810", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [33122, "SRR29654156", "SRX25158188", "SRS21848810", "SRP517033", "PRJNA1129880", "Neutrophil immune profile guides spinal cord regeneration in zebrafish", "GSE271113", "Transcriptome Analysis", "Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Funda\u00e7\u00e5o para a Ci\u00eancia e Tecnologia FCT  Portugal", null, "pubmed:38925414", null, "Neutrophils mpx+  uninjured  DMSO  biol rep 1", "GSM8369969", null, "tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing", "Neutrophils mpx+  uninjured  DMSO  biol rep 1", "Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script", "Neutrophils mpx:GFP+", "At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", "Zebrafish embryos were raised at 28.5\u00baC in E3 media with Methylene blue", "cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO", "GSM8369969", "GSM8369969: Neutrophils mpx+  uninjured  DMSO  biol rep 1; Danio rerio; RNA Seq", "GSM8369969 r1", "GSM8369969", "1", "Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5\u00baC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP517033", null, null, "IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_DMSO_-003_cbc.fastq.gz", "fastq", 55531080.0, 925518.0, "GSM8369969 r4", "0:60", "A:20538193;C:10150017;G:10949669;T:13888674;N:4527", 60, null, null, null, 20538193, 10150017, 10949669, 13888674, 4527, "SRX25158188", "SRS21848810", "SRA1913211", "Instituto de Medicina Molecular", "Instituto de Medicina Molecular", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "single_cell_plate", "celseq", null, "Portugal", "2024-06-29", "Larval", "Larval", "Blood", "Hematopoietic System"], [38073, "SRR1531483", "SRX665263", "SRS670077", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "18 somites stage  straightened  secti1d tail to head", "GSM1448820", null, "tissue:deyolked embryo  head removed|Stage:18 somites|sectioning direction:tail to head|section thickness:24 \u00b5m|embedding strategy:deyolked and straightened embryo", "18 somites stage  straightened  secti1d tail to head", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "deyolked embryo  head removed", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:18 somites|sectioning direction:tail to head|section thickness:24 \u00b5m|embedding strategy:deyolked and straightened embryo", "GSM1448820", "GSM1448820: 18 somites stage  straightened  secti1d tail to head; Danio rerio; RNA Seq", "GSM1448820", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448820", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_18ss_TH_R2.fastq.gz dr_18ss_TH_R1.fastq.gz", "fastq fastq", 15779230884.0, 154698342.0, "GSM1448820 r1", "0:51 1:51", "A:3451000604;C:2392800593;G:2522666152;T:7412137093;N:626442", 51, 51, null, null, 3451000604, 2392800593, 2522666152, 7412137093, 626442, "SRX665263", "SRS670077", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.11555, 0.70031, 0.08647, 0.12212, 0.98238, 0.78946, 0.48905, 0.5514, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38074, "SRR1531482", "SRX665262", "SRS670076", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "15 somites stage  straightened  secti1d tail to head  replicate", "GSM1448819", null, "tissue:deyolked embryo|Stage:15 somites|sectioning direction:tail to head|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "15 somites stage  straightened  secti1d tail to head  replicate", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "deyolked embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:15 somites|sectioning direction:tail to head|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "GSM1448819", "GSM1448819: 15 somites stage  straightened  secti1d tail to head  replicate; Danio rerio; RNA Seq", "GSM1448819", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448819", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_15ss_TH2_R2.fastq.gz dr_15ss_TH2_R1.fastq.gz", "fastq fastq", 4502603442.0, 44143171.0, "GSM1448819 r1", "0:51 1:51", "A:1010801791;C:688133305;G:712006267;T:2047960758;N:43701321", 51, 51, null, null, 1010801791, 688133305, 712006267, 2047960758, 43701321, "SRX665262", "SRS670076", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.0903, 0.78618, 0.08054, 0.12953, 0.98703, 0.78046, 0.53574, 0.52775, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38075, "SRR1531481", "SRX665261", "SRS670075", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "sections 97 108 for samples dr 15ss TH and dr 15ss HT", "GSM1448818", null, "tissue:deyolked embryo|Stage:15 somites|sectioning direction:head to tail and tail to head|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "sections 97 108 for samples dr 15ss TH and dr 15ss HT", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "deyolked embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:15 somites|sectioning direction:head to tail and tail to head|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "GSM1448818", "GSM1448818: sections 97 108 for samples dr 15ss TH and dr 15ss HT; Danio rerio; RNA Seq", "GSM1448818", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448818", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_15ss_TH97-108_HT97-108_R2.fastq.gz dr_15ss_TH97-108_HT97-108_R1.fastq.gz", "fastq fastq", 472071606.0, 4628153.0, "GSM1448818 r1", "0:51 1:51", "A:108013079;C:76852222;G:73612321;T:208300498;N:5293486", 51, 51, null, null, 108013079, 76852222, 73612321, 208300498, 5293486, "SRX665261", "SRS670075", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.06997, 0.71056, 0.06103, 0.12966, 0.9865, 0.79446, 0.53118, 0.53673, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38076, "SRR1531480", "SRX665260", "SRS670074", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "15 somites stage  straightened  secti1d tail to head", "GSM1448817", null, "tissue:deyolked embryo|Stage:15 somites|sectioning direction:tail to head|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "15 somites stage  straightened  secti1d tail to head", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "deyolked embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:15 somites|sectioning direction:tail to head|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "GSM1448817", "GSM1448817: 15 somites stage  straightened  secti1d tail to head; Danio rerio; RNA Seq", "GSM1448817", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448817", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_15ss_TH_R1.fastq.gz dr_15ss_TH_R2.fastq.gz", "fastq fastq", 3381229314.0, 33149307.0, "GSM1448817 r1", "0:51 1:51", "A:806003850;C:517726785;G:527487361;T:1491678004;N:38333314", 51, 51, null, null, 806003850, 517726785, 527487361, 1491678004, 38333314, "SRX665260", "SRS670074", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.06812, 0.69273, 0.05849, 0.1511, 0.98502, 0.7834, 0.47808, 0.53868, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38077, "SRR1531479", "SRX665259", "SRS670073", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "15 somites stage  straightened  secti1d head to tail", "GSM1448816", null, "tissue:deyolked embryo|Stage:15 somites|sectioning direction:head to tail|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "15 somites stage  straightened  secti1d head to tail", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "deyolked embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:15 somites|sectioning direction:head to tail|section thickness:18 \u00b5m|embedding strategy:deyolked and straightened embryo", "GSM1448816", "GSM1448816: 15 somites stage  straightened  secti1d head to tail; Danio rerio; RNA Seq", "GSM1448816", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448816", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_15ss_HT_R1.fastq.gz dr_15ss_HT_R2.fastq.gz", "fastq fastq", 3476174076.0, 34080138.0, "GSM1448816 r1", "0:51 1:51", "A:800519794;C:540890287;G:554165272;T:1542680760;N:37917963", 51, 51, null, null, 800519794, 540890287, 554165272, 1542680760, 37917963, "SRX665259", "SRS670073", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.06769, 0.70036, 0.05945, 0.13184, 0.98849, 0.79026, 0.50058, 0.57003, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38078, "SRR1531477", "SRX665258", "SRS670072", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "15 somite stage  secti1d from right to left", "GSM1448815", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:right left|section thickness:18 \u00b5m|embedding strategy:intact embryo", "15 somite stage  secti1d from right to left", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:15 somites|sectioning direction:right left|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448815", "GSM1448815: 15 somite stage  secti1d from right to left; Danio rerio; RNA Seq", "GSM1448815", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448815", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_15ss_RL_R1.fastq.gz dr_15ss_RL_R2.fastq.gz", "fastq fastq", 3840123336.0, 37648268.0, "GSM1448815 r1", "0:51 1:51", "A:915153174;C:577478134;G:648196113;T:1695635476;N:3660439", 51, 51, null, null, 915153174, 577478134, 648196113, 1695635476, 3660439, "SRX665258", "SRS670072", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.05313, 0.71589, 0.0419, 0.15174, 0.97717, 0.77484, 0.5218, 0.45828, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [38079, "SRR1531478", "SRX665258", "SRS670072", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "15 somite stage  secti1d from right to left", "GSM1448815", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:right left|section thickness:18 \u00b5m|embedding strategy:intact embryo", "15 somite stage  secti1d from right to left", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:15 somites|sectioning direction:right left|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448815", "GSM1448815: 15 somite stage  secti1d from right to left; Danio rerio; RNA Seq", "GSM1448815", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448815", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, "instrument model:Illumina MiSeq", "miseq_dr_15ss_RL_R1.fastq.gz miseq_dr_15ss_RL_R2.fastq.gz", "fastq fastq", 619303490.0, 1235999.0, "GSM1448815 r2", "0:251 1:250.06", "A:196814024;C:126079066;G:111585151;T:184825248;N:1", 251, 250, null, null, 196814024, 126079066, 111585151, 184825248, 1, "SRX665258", "SRS670072", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.37674, 0.6743, 0.06734, 0.08523, 0.92516, 0.86196, 0.56151, 0.54745, 251, 251, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [38080, "SRR1531475", "SRX665257", "SRS670070", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "15 somite stage  secti1d from left to right", "GSM1448814", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:left right|section thickness:18 \u00b5m|embedding strategy:intact embryo", "15 somite stage  secti1d from left to right", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:15 somites|sectioning direction:left right|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448814", "GSM1448814: 15 somite stage  secti1d from left to right; Danio rerio; RNA Seq", "GSM1448814", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448814", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_15ss_LR_R2.fastq.gz dr_15ss_LR_R1.fastq.gz", "fastq fastq", 2077803342.0, 20370621.0, "GSM1448814 r1", "0:51 1:51", "A:487276259;C:320933398;G:342175116;T:925418636;N:1999933", 51, 51, null, null, 487276259, 320933398, 342175116, 925418636, 1999933, "SRX665257", "SRS670070", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.04544, 0.77533, 0.03741, 0.15439, 0.98435, 0.77662, 0.56397, 0.57005, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [38081, "SRR1531476", "SRX665257", "SRS670070", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "15 somite stage  secti1d from left to right", "GSM1448814", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:left right|section thickness:18 \u00b5m|embedding strategy:intact embryo", "15 somite stage  secti1d from left to right", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:15 somites|sectioning direction:left right|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448814", "GSM1448814: 15 somite stage  secti1d from left to right; Danio rerio; RNA Seq", "GSM1448814", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448814", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, "instrument model:Illumina MiSeq", "miseq_dr_15ss_LR_R1.fastq.gz miseq_dr_15ss_LR_R2.fastq.gz", "fastq fastq", 648479770.0, 1294232.0, "GSM1448814 r2", "0:251 1:250.05", "A:208271519;C:133135452;G:114142609;T:192930139;N:51", 251, 250, null, null, 208271519, 133135452, 114142609, 192930139, 51, "SRX665257", "SRS670070", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.34992, 0.64011, 0.08713, 0.16967, 0.92103, 0.83853, 0.54292, 0.52547, 251, 250, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [38082, "SRR1531473", "SRX665256", "SRS670071", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "15 somite stage  secti1d from dorsal to ventral end", "GSM1448813", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|embedding strategy:intact embryo", "15 somite stage  secti1d from dorsal to ventral end", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448813", "GSM1448813: 15 somite stage  secti1d from dorsal to ventral end; Danio rerio; RNA Seq", "GSM1448813", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", "GEO Accession:GSM1448813", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP045064", null, null, "dr_15ss_DV_R1.fastq.gz dr_15ss_DV_R2.fastq.gz", "fastq fastq", 2516804610.0, 24674555.0, "GSM1448813 r1", "0:51 1:51", "A:579818006;C:406550753;G:379205422;T:1129932140;N:21298289", 51, 51, null, null, 579818006, 406550753, 379205422, 1129932140, 21298289, "SRX665256", "SRS670071", "SRA177126", "GEO", "Hubrecht Institute", 2, 0.04189, 0.74891, 0.03368, 0.12625, 0.98695, 0.78423, 0.46823, 0.53429, 51, 51, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2014-07-29", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [38083, "SRR1531474", "SRX665256", "SRS670071", "SRP045064", "PRJNA256975", "Genome wide RNA tomography in the zebrafish embryo", "GSE59873", "Other", "Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.", null, "pubmed:25417113", null, "15 somite stage  secti1d from dorsal to ventral end", "GSM1448813", null, "tissue:whole embryo|Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|embedding strategy:intact embryo", "15 somite stage  secti1d from dorsal to ventral end", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "whole embryo", "Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012", null, "Stage:15 somites|sectioning direction:dorsal ventral|section thickness:18 \u00b5m|embedding strategy:intact embryo", "GSM1448813", "GSM1448813: 15 somite stage  secti1d from dorsal to ventral end; Danio rerio; RNA Seq", "GSM1448813", null, "1", "RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  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