rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
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,,zebrafish 14dpi heart3,GSM7717530,,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.  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,,tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi,GSM7717530,GSM7717530: zebrafish 14dpi heart3; Danio rerio; RNA Seq,GSM7717530 r1,GSM7717530,1,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,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP455780,,loader:fastq load.py|options:  allowEarlyFileEnd,DB14zf4_R1.fq DB14zf4_R2.fq,fastq fastq,571157496.0,7312520.0,GSM7717530 r1,,A:132329616;C:53169305;G:72431948;T:313058610;N:168017,,,,,132329616,53169305,72431948,313058610,168017,SRX21410761,SRS18649243,SRA1751823,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.01414,0.679,0.01413,0.08289,1.0,0.98395,,0.48915,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25229,SRR25685573,SRX21410760,SRS18649241,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,,zebrafish 14dpi heart2,GSM7717529,,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.  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,,tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi,GSM7717529,GSM7717529: zebrafish 14dpi heart2; Danio rerio; RNA Seq,GSM7717529 r1,GSM7717529,1,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,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP455780,,loader:fastq load.py|options:  allowEarlyFileEnd,DB14zf3_R1.fq DB14zf3_R2.fq,fastq fastq,97890367.0,1292037.0,GSM7717529 r1,,A:21637243;C:8563955;G:12004508;T:55662880;N:21781,,,,,21637243,8563955,12004508,55662880,21781,SRX21410760,SRS18649241,SRA1751823,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.0,0.689,0.0,0.07655,1.0,0.99831,,0.63709,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25230,SRR25685574,SRX21410759,SRS18649242,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,,zebrafish 14dpi heart1,GSM7717528,,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.  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,,tissue:adult heart|transgenic background:wildtype|section thickness:Took every section|section direction:from injured area into the remote myocardium|treatment:cryoinjury|timepoint:14dpi,GSM7717528,GSM7717528: zebrafish 14dpi heart1; Danio rerio; RNA Seq,GSM7717528 r1,GSM7717528,1,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,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP455780,,loader:fastq load.py|options:  allowEarlyFileEnd,DB14zf1_R1.fq DB14zf1_R2.fq,fastq fastq,1031757474.0,7257847.0,GSM7717528 r1,,A:276216587;C:146620316;G:184052670;T:423474577;N:1393324,,,,,276216587,146620316,184052670,423474577,1393324,SRX21410759,SRS18649242,SRA1751823,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.04176,0.6198,0.03023,0.08234,0.99894,0.88885,0.64556,0.53126,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25231,SRR25685575,SRX21410758,SRS18649240,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,,zebrafish 7dpi heart3,GSM7717527,,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,,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.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP455780,,loader:fastq load.py|options:  allowEarlyFileEnd,D37DPIZF3_R1.fq D37DPIZF3_R2.fq,fastq fastq,898901460.0,7585924.0,GSM7717527 r1,,A:236935836;C:100995680;G:128458892;T:431620821;N:890231,,,,,236935836,100995680,128458892,431620821,890231,SRX21410758,SRS18649240,SRA1751823,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.12082,0.70068,0.10594,0.1234,0.99983,0.90136,0.875,0.48346,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25232,SRR25685576,SRX21410757,SRS18649239,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,,zebrafish 7dpi heart2,GSM7717526,,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,,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.  Cell Reports  2012; also  see: Junker et al.  2014  Cell,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP455780,,loader:fastq load.py|options:  allowEarlyFileEnd,D27DPIZF2_R1.fq D27DPIZF2_R2.fq,fastq fastq,1060429257.0,7609110.0,GSM7717526 r1,,A:283107752;C:130181128;G:159305328;T:486464477;N:1370572,,,,,283107752,130181128,159305328,486464477,1370572,SRX21410757,SRS18649239,SRA1751823,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.19472,0.68783,0.17584,0.16739,0.99967,0.85628,0.44,0.56319,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25233,SRR25685577,SRX21410756,SRS18649238,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,,zebrafish 7dpi heart1,GSM7717525,,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,,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,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP455780,,loader:fastq load.py|options:  allowEarlyFileEnd,D17DPIZF1_R1.fq D17DPIZF1_R2.fq,fastq fastq,1073044507.0,7624815.0,GSM7717525 r1,,A:288576038;C:136858647;G:170330711;T:475869519;N:1409592,,,,,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,,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,,zebrafish 3dpi heart3,GSM7717524,,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,,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,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP455780,,,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,,,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,,0.53909,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,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,,zebrafish 3dpi heart2,GSM7717523,,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,,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,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP455780,,,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,,,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,,0.56367,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,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,,zebrafish 3dpi heart1,GSM7717522,,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,,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,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP455780,,,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,,,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,,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,,hmga1a mutant plate 4,GSM7728123,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,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,,hmga1a mutant plate 4,GSM7728123,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,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,,hmga1a mutant plate 4,GSM7728123,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,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,,hmga1a mutant plate 4,GSM7728123,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,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,,hmga1a mutant plate 3,GSM7728122,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,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,,hmga1a mutant plate 3,GSM7728122,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,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,,hmga1a mutant plate 3,GSM7728122,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,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,,hmga1a mutant plate 3,GSM7728122,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,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,,wildtype plate 3,GSM7728121,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,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,,wildtype plate 3,GSM7728121,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,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,,wildtype plate 3,GSM7728121,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,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,,wildtype plate 3,GSM7728121,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,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,,wildtype plate 2,GSM7728120,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,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,,wildtype plate 2,GSM7728120,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,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,,wildtype plate 2,GSM7728120,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,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,,wildtype plate 2,GSM7728120,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,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,,hmga1a mutant plate 2,GSM7728119,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,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,,hmga1a mutant plate 2,GSM7728119,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,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,,hmga1a mutant plate 2,GSM7728119,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,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,,hmga1a mutant plate 2,GSM7728119,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,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,,hmga1a mutant plate 1,GSM7728118,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,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,,hmga1a mutant plate 1,GSM7728118,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,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,,hmga1a mutant plate 1,GSM7728118,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,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,,hmga1a mutant plate 1,GSM7728118,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,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,,wildtype plate 1,GSM7728117,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,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,,wildtype plate 1,GSM7728117,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,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,,wildtype plate 1,GSM7728117,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,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,,wildtype plate 1,GSM7728117,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP456323,,,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,,,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,,Netherlands,2023-08-22,Adult,Adult,Heart,Cardiovascular System
73951,SRR23290994,SRX19234275,SRS16638733,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 21dpi 2,GSM7016815,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi|geo loc name:missing|collection date:missing,zfCM 21dpi 2,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi,GSM7016815,GSM7016815: zfCM 21dpi 2; Danio rerio; RNA Seq,GSM7016815 r1,GSM7016815,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-PN-s041_H7L35BGXM_S4_L001_R1_001.fastq.gz HUB-PN-s041_H7L35BGXM_S4_L001_R2_001.fastq.gz,fastq fastq,858173876.0,9978766.0,GSM7016815 r1,0:26 1:60,A:213059809;C:160771814;G:156105199;T:328218073;N:18981,26,60,,,213059809,160771814,156105199,328218073,18981,SRX19234275,SRS16638733,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11426,0.88222,0.10668,0.29657,0.99149,0.8355,0.60863,0.67263,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73952,SRR23290995,SRX19234275,SRS16638733,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 21dpi 2,GSM7016815,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi|geo loc name:missing|collection date:missing,zfCM 21dpi 2,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi,GSM7016815,GSM7016815: zfCM 21dpi 2; Danio rerio; RNA Seq,GSM7016815 r1,GSM7016815,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-PN-s041_H7L35BGXM_S4_L002_R1_001.fastq.gz HUB-PN-s041_H7L35BGXM_S4_L002_R2_001.fastq.gz,fastq fastq,843721318.0,9810713.0,GSM7016815 r2,0:26 1:60,A:208714473;C:157371099;G:155893107;T:321724427;N:18212,26,60,,,208714473,157371099,155893107,321724427,18212,SRX19234275,SRS16638733,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11232,0.8799,0.10497,0.29809,0.99123,0.83621,0.66836,0.66521,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73953,SRR23290996,SRX19234275,SRS16638733,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 21dpi 2,GSM7016815,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi|geo loc name:missing|collection date:missing,zfCM 21dpi 2,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi,GSM7016815,GSM7016815: zfCM 21dpi 2; Danio rerio; RNA Seq,GSM7016815 r1,GSM7016815,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-PN-s041_H7L35BGXM_S4_L003_R1_001.fastq.gz HUB-PN-s041_H7L35BGXM_S4_L003_R2_001.fastq.gz,fastq fastq,864128860.0,10048010.0,GSM7016815 r3,0:26 1:60,A:214256028;C:161957471;G:157308166;T:330585259;N:21936,26,60,,,214256028,161957471,157308166,330585259,21936,SRX19234275,SRS16638733,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.1147,0.88514,0.10704,0.29827,0.99105,0.83321,0.67314,0.65637,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73954,SRR23290997,SRX19234275,SRS16638733,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 21dpi 2,GSM7016815,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi|geo loc name:missing|collection date:missing,zfCM 21dpi 2,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi,GSM7016815,GSM7016815: zfCM 21dpi 2; Danio rerio; RNA Seq,GSM7016815 r1,GSM7016815,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-PN-s041_H7L35BGXM_S4_L004_R1_001.fastq.gz HUB-PN-s041_H7L35BGXM_S4_L004_R2_001.fastq.gz,fastq fastq,862094960.0,10024360.0,GSM7016815 r4,0:26 1:60,A:212975380;C:160923939;G:159237695;T:328939876;N:18070,26,60,,,212975380,160923939,159237695,328939876,18070,SRX19234275,SRS16638733,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11191,0.88105,0.10467,0.2945,0.99151,0.83623,0.67428,0.67156,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73955,SRR23290998,SRX19234274,SRS16638732,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 4,GSM7016814,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 4,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016814,GSM7016814: zfCM 7dpi 4; Danio rerio; RNA Seq,GSM7016814 r1,GSM7016814,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-PN-s039_H7L35BGXM_S3_L001_R1_001.fastq.gz HUB-PN-s039_H7L35BGXM_S3_L001_R2_001.fastq.gz,fastq fastq,839750096.0,9764536.0,GSM7016814 r1,0:26 1:60,A:207245393;C:152642612;G:152075698;T:327767742;N:18651,26,60,,,207245393,152642612,152075698,327767742,18651,SRX19234274,SRS16638732,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.10807,0.88063,0.1011,0.31218,0.99133,0.81844,0.57963,0.58371,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73956,SRR23290999,SRX19234274,SRS16638732,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 4,GSM7016814,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 4,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016814,GSM7016814: zfCM 7dpi 4; Danio rerio; RNA Seq,GSM7016814 r1,GSM7016814,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-PN-s039_H7L35BGXM_S3_L002_R1_001.fastq.gz HUB-PN-s039_H7L35BGXM_S3_L002_R2_001.fastq.gz,fastq fastq,824555530.0,9587855.0,GSM7016814 r2,0:26 1:60,A:202762477;C:149247401;G:151695233;T:320832302;N:18117,26,60,,,202762477,149247401,151695233,320832302,18117,SRX19234274,SRS16638732,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.10764,0.87478,0.1005,0.31049,0.99101,0.81929,0.58127,0.51321,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73957,SRR23291000,SRX19234274,SRS16638732,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 4,GSM7016814,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 4,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016814,GSM7016814: zfCM 7dpi 4; Danio rerio; RNA Seq,GSM7016814 r1,GSM7016814,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-PN-s039_H7L35BGXM_S3_L003_R1_001.fastq.gz HUB-PN-s039_H7L35BGXM_S3_L003_R2_001.fastq.gz,fastq fastq,845111766.0,9826881.0,GSM7016814 r3,0:26 1:60,A:208286833;C:153694024;G:153159692;T:329951816;N:19401,26,60,,,208286833,153694024,153159692,329951816,19401,SRX19234274,SRS16638732,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.1087,0.88111,0.10148,0.31291,0.99068,0.81698,0.55014,0.58727,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73958,SRR23291001,SRX19234274,SRS16638732,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 4,GSM7016814,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 4,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016814,GSM7016814: zfCM 7dpi 4; Danio rerio; RNA Seq,GSM7016814 r1,GSM7016814,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-PN-s039_H7L35BGXM_S3_L004_R1_001.fastq.gz HUB-PN-s039_H7L35BGXM_S3_L004_R2_001.fastq.gz,fastq fastq,842710216.0,9798956.0,GSM7016814 r4,0:26 1:60,A:206896294;C:152644705;G:155014140;T:328138108;N:16969,26,60,,,206896294,152644705,155014140,328138108,16969,SRX19234274,SRS16638732,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.10766,0.87731,0.10058,0.31053,0.99119,0.81781,0.57185,0.57715,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73959,SRR23291002,SRX19234273,SRS16638731,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 21dpi 1,GSM7016813,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi|geo loc name:missing|collection date:missing,zfCM 21dpi 1,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi,GSM7016813,GSM7016813: zfCM 21dpi 1; Danio rerio; RNA Seq,GSM7016813 r1,GSM7016813,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-PN-025_HCMYKBGXC_S8_L001_R1_001.fastq.gz HUB-PN-025_HCMYKBGXC_S8_L001_R2_001.fastq.gz,fastq fastq,638322358.0,7422353.0,GSM7016813 r1,0:26 1:60,A:152993677;C:129279491;G:116490423;T:238075133;N:1483634,26,60,,,152993677,129279491,116490423,238075133,1483634,SRX19234273,SRS16638731,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.1186,0.92133,0.11281,0.53473,0.99391,0.89818,0.6282,0.56941,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73960,SRR23291003,SRX19234273,SRS16638731,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 21dpi 1,GSM7016813,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi|geo loc name:missing|collection date:missing,zfCM 21dpi 1,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi,GSM7016813,GSM7016813: zfCM 21dpi 1; Danio rerio; RNA Seq,GSM7016813 r1,GSM7016813,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-PN-025_HCMYKBGXC_S8_L002_R1_001.fastq.gz HUB-PN-025_HCMYKBGXC_S8_L002_R2_001.fastq.gz,fastq fastq,633345022.0,7364477.0,GSM7016813 r2,0:26 1:60,A:150874121;C:127629476;G:118171343;T:235389766;N:1280316,26,60,,,150874121,127629476,118171343,235389766,1280316,SRX19234273,SRS16638731,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11665,0.91596,0.11139,0.53318,0.99425,0.89822,0.64949,0.56009,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73961,SRR23291004,SRX19234273,SRS16638731,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 21dpi 1,GSM7016813,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi|geo loc name:missing|collection date:missing,zfCM 21dpi 1,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi,GSM7016813,GSM7016813: zfCM 21dpi 1; Danio rerio; RNA Seq,GSM7016813 r1,GSM7016813,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-PN-025_HCMYKBGXC_S8_L003_R1_001.fastq.gz HUB-PN-025_HCMYKBGXC_S8_L003_R2_001.fastq.gz,fastq fastq,643723416.0,7485156.0,GSM7016813 r3,0:26 1:60,A:154277144;C:130529094;G:117635488;T:240275453;N:1006237,26,60,,,154277144,130529094,117635488,240275453,1006237,SRX19234273,SRS16638731,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11809,0.9216,0.11258,0.53566,0.99397,0.89871,0.63435,0.55308,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73962,SRR23291005,SRX19234273,SRS16638731,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 21dpi 1,GSM7016813,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi|geo loc name:missing|collection date:missing,zfCM 21dpi 1,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:21dpi,GSM7016813,GSM7016813: zfCM 21dpi 1; Danio rerio; RNA Seq,GSM7016813 r1,GSM7016813,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-PN-025_HCMYKBGXC_S8_L004_R1_001.fastq.gz HUB-PN-025_HCMYKBGXC_S8_L004_R2_001.fastq.gz,fastq fastq,632759362.0,7357667.0,GSM7016813 r4,0:26 1:60,A:150797181;C:127674217;G:117974605;T:235361625;N:951734,26,60,,,150797181,127674217,117974605,235361625,951734,SRX19234273,SRS16638731,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11662,0.91609,0.11147,0.53237,0.99381,0.89775,0.65781,0.55524,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73963,SRR23291006,SRX19234272,SRS16638730,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 3,GSM7016812,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 3,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016812,GSM7016812: zfCM 7dpi 3; Danio rerio; RNA Seq,GSM7016812 r1,GSM7016812,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,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,GSM7016812 r1,0:26 1:60,A:240334465;C:174255952;G:184260587;T:330943403;N:205121,26,60,,,240334465,174255952,184260587,330943403,205121,SRX19234272,SRS16638730,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11116,0.87404,0.10307,0.43901,0.99178,0.93034,0.6268,0.44639,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73964,SRR23291007,SRX19234272,SRS16638730,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 3,GSM7016812,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 3,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016812,GSM7016812: zfCM 7dpi 3; Danio rerio; RNA Seq,GSM7016812 r1,GSM7016812,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,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,GSM7016812 r2,0:26 1:60,A:251121714;C:184449811;G:201317783;T:350692225;N:243363,26,60,,,251121714,184449811,201317783,350692225,243363,SRX19234272,SRS16638730,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11269,0.87873,0.10426,0.44461,0.99172,0.92506,0.6241,0.4506,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73965,SRR23291008,SRX19234272,SRS16638730,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 3,GSM7016812,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 3,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016812,GSM7016812: zfCM 7dpi 3; Danio rerio; RNA Seq,GSM7016812 r1,GSM7016812,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,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,GSM7016812 r3,0:26 1:60,A:247983556;C:179564753;G:190342582;T:341858456;N:183685,26,60,,,247983556,179564753,190342582,341858456,183685,SRX19234272,SRS16638730,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11176,0.87161,0.10342,0.43986,0.99155,0.93026,0.63442,0.44405,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73966,SRR23291009,SRX19234272,SRS16638730,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 3,GSM7016812,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 3,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016812,GSM7016812: zfCM 7dpi 3; Danio rerio; RNA Seq,GSM7016812 r1,GSM7016812,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,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,GSM7016812 r4,0:26 1:60,A:205538880;C:148510556;G:161196381;T:282964175;N:160774,26,60,,,205538880,148510556,161196381,282964175,160774,SRX19234272,SRS16638730,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11014,0.87018,0.10209,0.43668,0.9921,0.93346,0.56645,0.44683,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73967,SRR23291010,SRX19234271,SRS16638729,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 2,GSM7016811,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 2,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016811,GSM7016811: zfCM 7dpi 2; Danio rerio; RNA Seq,GSM7016811 r1,GSM7016811,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,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,GSM7016811 r1,0:26 1:60,A:213590554;C:148614157;G:163804315;T:279996916;N:172592,26,60,,,213590554,148614157,163804315,279996916,172592,SRX19234271,SRS16638729,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.10778,0.79221,0.1011,0.39378,0.99299,0.93695,0.65894,0.39542,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73968,SRR23291011,SRX19234271,SRS16638729,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 2,GSM7016811,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 2,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016811,GSM7016811: zfCM 7dpi 2; Danio rerio; RNA Seq,GSM7016811 r1,GSM7016811,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,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,GSM7016811 r2,0:26 1:60,A:227213153;C:160851586;G:182364146;T:303951184;N:214217,26,60,,,227213153,160851586,182364146,303951184,214217,SRX19234271,SRS16638729,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11066,0.80318,0.10409,0.40131,0.99289,0.9333,0.66859,0.40896,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73969,SRR23291012,SRX19234271,SRS16638729,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 2,GSM7016811,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 2,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016811,GSM7016811: zfCM 7dpi 2; Danio rerio; RNA Seq,GSM7016811 r1,GSM7016811,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,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,GSM7016811 r3,0:26 1:60,A:220300204;C:153061412;G:168938657;T:289375449;N:160138,26,60,,,220300204,153061412,168938657,289375449,160138,SRX19234271,SRS16638729,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.10977,0.78663,0.1033,0.39172,0.99297,0.93669,0.64493,0.36881,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73970,SRR23291013,SRX19234271,SRS16638729,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 2,GSM7016811,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 2,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016811,GSM7016811: zfCM 7dpi 2; Danio rerio; RNA Seq,GSM7016811 r1,GSM7016811,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,HUB-DB-005_HNWVVBGX9_S4_L004_R1_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L004_R2_001.fastq.gz,fastq fastq,692573136.0,8053176.0,GSM7016811 r4,0:26 1:60,A:182418113;C:126757471;G:143869511;T:239393143;N:134898,26,60,,,182418113,126757471,143869511,239393143,134898,SRX19234271,SRS16638729,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.10826,0.81364,0.10182,0.40464,0.9931,0.94034,0.66059,0.40686,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73971,SRR23291015,SRX19234270,SRS16638728,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 1,GSM7016810,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 1,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016810,GSM7016810: zfCM 7dpi 1; Danio rerio; RNA Seq,GSM7016810 r1,GSM7016810,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,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,GSM7016810 r1,0:26 1:60,A:125045012;C:89627491;G:85413855;T:171466861;N:149815,26,60,,,125045012,89627491,85413855,171466861,149815,SRX19234270,SRS16638728,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.10906,0.67997,0.10214,0.30398,0.99117,0.94209,0.6357,0.45559,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73972,SRR23291016,SRX19234270,SRS16638728,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 1,GSM7016810,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 1,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016810,GSM7016810: zfCM 7dpi 1; Danio rerio; RNA Seq,GSM7016810 r1,GSM7016810,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,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,GSM7016810 r2,0:26 1:60,A:131516821;C:92202683;G:88685608;T:176824985;N:142841,26,60,,,131516821,92202683,88685608,176824985,142841,SRX19234270,SRS16638728,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.11042,0.68087,0.10314,0.3043,0.99145,0.94882,0.5723,0.46048,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73973,SRR23291017,SRX19234270,SRS16638728,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 1,GSM7016810,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 1,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016810,GSM7016810: zfCM 7dpi 1; Danio rerio; RNA Seq,GSM7016810 r1,GSM7016810,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,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,GSM7016810 r3,0:26 1:60,A:108841476;C:77418215;G:73171345;T:148203998;N:100254,26,60,,,108841476,77418215,73171345,148203998,100254,SRX19234270,SRS16638728,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.10889,0.67068,0.10168,0.29526,0.99117,0.9471,0.66379,0.42801,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System
73974,SRR23291018,SRX19234270,SRS16638728,SRP420309,PRJNA929990,Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration,GSE224156,Other,Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied  little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad  a structure that regulates calcium handling and excitation contraction coupling  played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation  prevented cardiomegaly  and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.,,pubmed:37200435,,zfCM 7dpi 1,GSM7016810,,source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing,zfCM 7dpi 1,"Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced  unspliced or total reads.",Heart,Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi,GSM7016810,GSM7016810: zfCM 7dpi 1; Danio rerio; RNA Seq,GSM7016810 r1,GSM7016810,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol  the CEL seq2 protocol  is carried out with the aid of robotic liquid handlers. 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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP420309,,,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,GSM7016810 r4,0:26 1:60,A:135189083;C:94908231;G:92431583;T:182885125;N:125282,26,60,,,135189083,94908231,92431583,182885125,125282,SRX19234270,SRS16638728,SRA1583767,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",2,0.10989,0.68603,0.10295,0.30544,0.99119,0.94783,0.65617,0.41933,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2023-01-31,Undetermined,Undetermined,Heart,Cardiovascular System