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
40164,SRR2921973,SRX1432516,SRS1163508,SRP066192,PRJNA302179,Genome–wide transcriptional profiling with spatial resolution identifies Bone Morphogenetic Protein signaling as essential regulator of zebrafish cardiomyocyte regeneration.,GSE74652,Transcriptome Analysis,In contrast to mammals  zebrafish regenerate heart injuries via proliferation of cardiomyocytes located at the wound border. Here  we show that tomo seq can be used to identify whole genome transcriptional profiles of the injury zone  the border zone and the healthy myocardium. Interestingly  the border zone is characterized by the re expression of embryonic cardiac genes that are also activated post myocardial infarction in mouse and human  including targets of Bone Morphogenetic Protein BMP signaling. Endogenous BMP signaling has been reported to be detrimental to mammalian cardiac repair. In contrast  we find that genetic or chemical inhibition of BMP signaling in zebrafish reduces cardiomyocyte dedifferentiation and proliferation  ultimately compromising myocardial regeneration  while bmp2b overexpression is sufficient to enhance it. Our results provide a resource for further studies on the molecular regulation of cardiac regeneration and reveal intriguing differential cellular responses of cardiomyocytes to a conserved signaling pathway in regenerative versus non regenerative hearts. Overall design: To generate spatially resolved RNA seq data for injured zebrafish hearts 3 and 7 xxx post injury  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina NextSeq  using 75bp paired end sequencing.,,pubmed:26748692,,zebrafish heart WT 7dpi #1,GSM1924888,,source name:cryoinjured ventricle of the heart|tissue:adult heart|sectioning direction:injury area   uninjured  remote myocardium|sectioning thickness:12 µm|embedding strategy:extracted heart at 7 days post cryoinjury,zebrafish heart WT 7dpi #1,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,cryoinjured ventricle of the heart,Unfixed ventricle was embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see: Junker et al.  2014  Cell,,tissue:adult heart|sectioning direction:injury area   uninjured  remote myocardium|sectioning thickness:12 µm|embedding strategy:extracted heart at 7 days post cryoinjury,GSM1924888,GSM1924888: zebrafish heart WT 7dpi #1; Danio rerio; RNA Seq,GSM1924888,,1,RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see: Junker et al.  2014  Cell,GEO Accession:GSM1924888,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP066192,,,FKHEART7_R1.fastq.gz FKHEART7_R2.fastq.gz,fastq fastq,3128649900.0,20745605.0,GSM1924888 r1,0:75.43 1:75.38,A:1025473014;C:388501715;G:410501025;T:1304153289;N:20857,75,75,,,1025473014,388501715,410501025,1304153289,20857,SRX1432516,SRS1163508,SRA311639,GEO,"Jeroen Bakkers, Hubrecht Institute",2,0.31194,0.62458,0.26968,0.18109,0.99308,0.89258,0.54708,0.5286,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,celseq,,Netherlands,2015-11-03,Adult,Adult,Heart,Cardiovascular System
40165,SRR2921972,SRX1432515,SRS1163510,SRP066192,PRJNA302179,Genome–wide transcriptional profiling with spatial resolution identifies Bone Morphogenetic Protein signaling as essential regulator of zebrafish cardiomyocyte regeneration.,GSE74652,Transcriptome Analysis,In contrast to mammals  zebrafish regenerate heart injuries via proliferation of cardiomyocytes located at the wound border. Here  we show that tomo seq can be used to identify whole genome transcriptional profiles of the injury zone  the border zone and the healthy myocardium. Interestingly  the border zone is characterized by the re expression of embryonic cardiac genes that are also activated post myocardial infarction in mouse and human  including targets of Bone Morphogenetic Protein BMP signaling. Endogenous BMP signaling has been reported to be detrimental to mammalian cardiac repair. In contrast  we find that genetic or chemical inhibition of BMP signaling in zebrafish reduces cardiomyocyte dedifferentiation and proliferation  ultimately compromising myocardial regeneration  while bmp2b overexpression is sufficient to enhance it. Our results provide a resource for further studies on the molecular regulation of cardiac regeneration and reveal intriguing differential cellular responses of cardiomyocytes to a conserved signaling pathway in regenerative versus non regenerative hearts. Overall design: To generate spatially resolved RNA seq data for injured zebrafish hearts 3 and 7 xxx post injury  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina NextSeq  using 75bp paired end sequencing.,,pubmed:26748692,,zebrafish heart WT 3dpi #1,GSM1924887,,source name:cryoinjured ventricle of the heart|tissue:adult heart|sectioning direction:injury area   uninjured  remote myocardium|sectioning thickness:12 µm|embedding strategy:extracted heart at 3 days post cryoinjury,zebrafish heart WT 3dpi #1,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,cryoinjured ventricle of the heart,Unfixed ventricle was embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.,RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see: Junker et al.  2014  Cell,,tissue:adult heart|sectioning direction:injury area   uninjured  remote myocardium|sectioning thickness:12 µm|embedding strategy:extracted heart at 3 days post cryoinjury,GSM1924887,GSM1924887: zebrafish heart WT 3dpi #1; Danio rerio; RNA Seq,GSM1924887,,1,RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see: Junker et al.  2014  Cell,GEO Accession:GSM1924887,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP066192,,,FKHEART3_R1.fastq.gz FKHEART3_R2.fastq.gz,fastq fastq,784558404.0,5209213.0,GSM1924887 r1,0:75.22 1:75.39,A:291009319;C:102718146;G:111606154;T:279144074;N:80711,75,75,,,291009319,102718146,111606154,279144074,80711,SRX1432515,SRS1163510,SRA311639,GEO,"Jeroen Bakkers, Hubrecht Institute",2,0.12872,0.82031,0.12623,0.08476,0.99997,0.82828,0.0,0.566,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,full_length,random_priming,unknown,sc,single_cell_plate,celseq,,Netherlands,2015-11-03,Adult,Adult,Heart,Cardiovascular System
59985,SRR12083057,SRX8610203,SRS6899881,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 012,GSM4635178,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 012,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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 order: 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 Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635178,GSM4635178: HUB DB 012; Danio rerio; RNA Seq,GSM4635178,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635178,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-012_H3HCLBGXC_S4_L001_R1_001.fastq.gz HUB-DB-012_H3HCLBGXC_S4_L001_R2_001.fastq.gz,fastq fastq,623629172.0,7251502.0,GSM4635178 r1,0:26 1:60,A:152264664;C:116216632;G:110007461;T:245137012;N:3403,26,60,,,152264664,116216632,110007461,245137012,3403,SRX8610203,SRS6899881,SRA1090808,GEO,Hubrecht,2,0.10748,0.88943,0.10172,0.27473,0.9931,0.82905,0.60372,0.48618,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59986,SRR12083058,SRX8610203,SRS6899881,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 012,GSM4635178,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 012,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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 order: 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 Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635178,GSM4635178: HUB DB 012; Danio rerio; RNA Seq,GSM4635178,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635178,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-012_H3HCLBGXC_S4_L002_R1_001.fastq.gz HUB-DB-012_H3HCLBGXC_S4_L002_R2_001.fastq.gz,fastq fastq,597918268.0,6952538.0,GSM4635178 r2,0:26 1:60,A:145156634;C:110841797;G:108031654;T:233885695;N:2488,26,60,,,145156634,110841797,108031654,233885695,2488,SRX8610203,SRS6899881,SRA1090808,GEO,Hubrecht,2,0.10741,0.88528,0.10165,0.27242,0.99289,0.82994,0.60407,0.47918,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59987,SRR12083059,SRX8610203,SRS6899881,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 012,GSM4635178,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 012,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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 order: 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 Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635178,GSM4635178: HUB DB 012; Danio rerio; RNA Seq,GSM4635178,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635178,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-012_H3HCLBGXC_S4_L003_R1_001.fastq.gz HUB-DB-012_H3HCLBGXC_S4_L003_R2_001.fastq.gz,fastq fastq,628530140.0,7308490.0,GSM4635178 r3,0:26 1:60,A:153358630;C:117237955;G:110777080;T:247131309;N:25166,26,60,,,153358630,117237955,110777080,247131309,25166,SRX8610203,SRS6899881,SRA1090808,GEO,Hubrecht,2,0.10839,0.88927,0.10281,0.27315,0.99316,0.8284,0.62118,0.46755,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59988,SRR12083060,SRX8610203,SRS6899881,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 012,GSM4635178,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 012,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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 order: 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 Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635178,GSM4635178: HUB DB 012; Danio rerio; RNA Seq,GSM4635178,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635178,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-012_H3HCLBGXC_S4_L004_R1_001.fastq.gz HUB-DB-012_H3HCLBGXC_S4_L004_R2_001.fastq.gz,fastq fastq,605801372.0,7044202.0,GSM4635178 r4,0:26 1:60,A:147072053;C:112438811;G:109075558;T:237165161;N:49789,26,60,,,147072053,112438811,109075558,237165161,49789,SRX8610203,SRS6899881,SRA1090808,GEO,Hubrecht,2,0.10729,0.88592,0.10142,0.2715,0.99318,0.83096,0.63628,0.47975,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59989,SRR12083053,SRX8610202,SRS6899880,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 011,GSM4635177,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 011,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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 order: 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 Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635177,GSM4635177: HUB DB 011; Danio rerio; RNA Seq,GSM4635177,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635177,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-011_H3HCLBGXC_S3_L001_R1_001.fastq.gz HUB-DB-011_H3HCLBGXC_S3_L001_R2_001.fastq.gz,fastq fastq,634797476.0,7381366.0,GSM4635177 r1,0:26 1:60,A:153195131;C:118480864;G:115080449;T:248037462;N:3570,26,60,,,153195131,118480864,115080449,248037462,3570,SRX8610202,SRS6899880,SRA1090808,GEO,Hubrecht,2,0.11082,0.89281,0.10414,0.28784,0.99204,0.82619,0.66824,0.50609,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59990,SRR12083054,SRX8610202,SRS6899880,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 011,GSM4635177,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 011,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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 order: 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 Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635177,GSM4635177: HUB DB 011; Danio rerio; RNA Seq,GSM4635177,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635177,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-011_H3HCLBGXC_S3_L002_R1_001.fastq.gz HUB-DB-011_H3HCLBGXC_S3_L002_R2_001.fastq.gz,fastq fastq,611046770.0,7105195.0,GSM4635177 r2,0:26 1:60,A:146818280;C:113612783;G:112799955;T:237813147;N:2605,26,60,,,146818280,113612783,112799955,237813147,2605,SRX8610202,SRS6899880,SRA1090808,GEO,Hubrecht,2,0.11194,0.89124,0.10494,0.28808,0.99275,0.83071,0.67141,0.50375,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59991,SRR12083055,SRX8610202,SRS6899880,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 011,GSM4635177,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 011,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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 order: 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 Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635177,GSM4635177: HUB DB 011; Danio rerio; RNA Seq,GSM4635177,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635177,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-011_H3HCLBGXC_S3_L003_R1_001.fastq.gz HUB-DB-011_H3HCLBGXC_S3_L003_R2_001.fastq.gz,fastq fastq,641591132.0,7460362.0,GSM4635177 r3,0:26 1:60,A:154776835;C:119807925;G:116219737;T:250759686;N:26949,26,60,,,154776835,119807925,116219737,250759686,26949,SRX8610202,SRS6899880,SRA1090808,GEO,Hubrecht,2,0.11171,0.8947,0.10479,0.29095,0.99233,0.82775,0.69148,0.50141,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59992,SRR12083056,SRX8610202,SRS6899880,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 011,GSM4635177,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 011,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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 order: 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 Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:prrx1b / |treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635177,GSM4635177: HUB DB 011; Danio rerio; RNA Seq,GSM4635177,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635177,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-011_H3HCLBGXC_S3_L004_R1_001.fastq.gz HUB-DB-011_H3HCLBGXC_S3_L004_R2_001.fastq.gz,fastq fastq,619988534.0,7209169.0,GSM4635177 r4,0:26 1:60,A:149057849;C:115334020;G:114131475;T:241414817;N:50373,26,60,,,149057849,115334020,114131475,241414817,50373,SRX8610202,SRS6899880,SRA1090808,GEO,Hubrecht,2,0.11255,0.89073,0.10573,0.28703,0.99283,0.83061,0.6874,0.50364,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59993,SRR12083049,SRX8610201,SRS6899879,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 010,GSM4635176,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 010,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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 order: 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 Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635176,GSM4635176: HUB DB 010; Danio rerio; RNA Seq,GSM4635176,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635176,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-010_H3HCLBGXC_S2_L001_R1_001.fastq.gz HUB-DB-010_H3HCLBGXC_S2_L001_R2_001.fastq.gz,fastq fastq,673568770.0,7832195.0,GSM4635176 r1,0:26 1:60,A:164220958;C:127417067;G:127429427;T:254497649;N:3669,26,60,,,164220958,127417067,127429427,254497649,3669,SRX8610201,SRS6899879,SRA1090808,GEO,Hubrecht,2,0.10904,0.86908,0.10146,0.28252,0.99086,0.83952,0.55689,0.51097,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59994,SRR12083050,SRX8610201,SRS6899879,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 010,GSM4635176,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 010,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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 order: 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 Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635176,GSM4635176: HUB DB 010; Danio rerio; RNA Seq,GSM4635176,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635176,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-010_H3HCLBGXC_S2_L002_R1_001.fastq.gz HUB-DB-010_H3HCLBGXC_S2_L002_R2_001.fastq.gz,fastq fastq,642282486.0,7468401.0,GSM4635176 r2,0:26 1:60,A:156140841;C:120979080;G:123582811;T:241577191;N:2563,26,60,,,156140841,120979080,123582811,241577191,2563,SRX8610201,SRS6899879,SRA1090808,GEO,Hubrecht,2,0.10877,0.86702,0.10115,0.2848,0.98961,0.84122,0.5621,0.48392,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59995,SRR12083051,SRX8610201,SRS6899879,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 010,GSM4635176,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 010,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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 order: 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 Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635176,GSM4635176: HUB DB 010; Danio rerio; RNA Seq,GSM4635176,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635176,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-010_H3HCLBGXC_S2_L003_R1_001.fastq.gz HUB-DB-010_H3HCLBGXC_S2_L003_R2_001.fastq.gz,fastq fastq,676661932.0,7868162.0,GSM4635176 r3,0:26 1:60,A:165121933;C:128034418;G:127770885;T:255708762;N:25934,26,60,,,165121933,128034418,127770885,255708762,25934,SRX8610201,SRS6899879,SRA1090808,GEO,Hubrecht,2,0.10987,0.87058,0.103,0.282,0.99109,0.83915,0.55503,0.51595,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59996,SRR12083052,SRX8610201,SRS6899879,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 010,GSM4635176,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 010,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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 order: 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 Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635176,GSM4635176: HUB DB 010; Danio rerio; RNA Seq,GSM4635176,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635176,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-010_H3HCLBGXC_S2_L004_R1_001.fastq.gz HUB-DB-010_H3HCLBGXC_S2_L004_R2_001.fastq.gz,fastq fastq,649298624.0,7549984.0,GSM4635176 r4,0:26 1:60,A:158062491;C:122309175;G:124562965;T:244314794;N:49199,26,60,,,158062491,122309175,124562965,244314794,49199,SRX8610201,SRS6899879,SRA1090808,GEO,Hubrecht,2,0.11052,0.86686,0.1033,0.2819,0.99052,0.84066,0.55805,0.50641,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59997,SRR12083045,SRX8610200,SRS6899878,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 009,GSM4635175,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 009,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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 order: 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 Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635175,GSM4635175: HUB DB 009; Danio rerio; RNA Seq,GSM4635175,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635175,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-009_H3HCLBGXC_S1_L001_R1_001.fastq.gz HUB-DB-009_H3HCLBGXC_S1_L001_R2_001.fastq.gz,fastq fastq,893990210.0,10395235.0,GSM4635175 r1,0:26 1:60,A:217651633;C:169265774;G:172112042;T:334955815;N:4946,26,60,,,217651633,169265774,172112042,334955815,4946,SRX8610200,SRS6899878,SRA1090808,GEO,Hubrecht,2,0.1006,0.81888,0.09561,0.29404,0.99318,0.83806,0.67678,0.52964,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59998,SRR12083046,SRX8610200,SRS6899878,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 009,GSM4635175,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 009,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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 order: 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 Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635175,GSM4635175: HUB DB 009; Danio rerio; RNA Seq,GSM4635175,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635175,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-009_H3HCLBGXC_S1_L002_R1_001.fastq.gz HUB-DB-009_H3HCLBGXC_S1_L002_R2_001.fastq.gz,fastq fastq,859084960.0,9989360.0,GSM4635175 r2,0:26 1:60,A:208058112;C:161872788;G:168851400;T:320298922;N:3738,26,60,,,208058112,161872788,168851400,320298922,3738,SRX8610200,SRS6899878,SRA1090808,GEO,Hubrecht,2,0.10183,0.81219,0.09621,0.29163,0.99281,0.83755,0.65329,0.52165,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
59999,SRR12083047,SRX8610200,SRS6899878,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 009,GSM4635175,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 009,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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 order: 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 Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635175,GSM4635175: HUB DB 009; Danio rerio; RNA Seq,GSM4635175,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635175,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-009_H3HCLBGXC_S1_L003_R1_001.fastq.gz HUB-DB-009_H3HCLBGXC_S1_L003_R2_001.fastq.gz,fastq fastq,903479192.0,10505572.0,GSM4635175 r3,0:26 1:60,A:220083458;C:171123276;G:173673810;T:338562517;N:36131,26,60,,,220083458,171123276,173673810,338562517,36131,SRX8610200,SRS6899878,SRA1090808,GEO,Hubrecht,2,0.10152,0.81676,0.09602,0.29263,0.99255,0.83717,0.63699,0.5171,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
60000,SRR12083048,SRX8610200,SRS6899878,SRP268691,PRJNA641676,Prrx1b restricts fibrosis and promotes Nrg1 dependent cardiomyocyte proliferation during zebrafish heart regeneration,GSE153170,Transcriptome Analysis,Fibroblasts are activated to repair the heart following injury. Fibroblast activation in the mammalian heart leads to a permanent fibrotic scar that impairs cardiac function. In other organisms  such as zebrafish  cardiac injury is followed by transient fibrosis and scar free regeneration. The mechanisms that drive scarring versus scar free regeneration are not well understood. Here  we show that the homeobox containing transcription factor Prrx1b is required for scar free regeneration of the zebrafish heart as the loss of Prrx1b results in excessive fibrosis and impaired cardiomyocyte proliferation. Through lineage tracing and single cell RNA sequencing we find that Prrx1b is activated in epicardial derived cells where it restricts TGFß ligand expression and collagen production. Furthermore  through combined in vitro experiments in human fetal epicardial derived cells and in vivo rescue experiments in zebrafish  we conclude that Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte proliferation. Collectively  these results indicate that Prrx1 is a key transcription factor that balances fibrosis and regeneration in the injured zebrafish heart. Overall design: Tgtcf21:mCherry positive cells n=1438 were collected from cryoinjured hearts of wild type n = 20 and prrx1b /  n=20 ventricles. All cells were sent for single cell RNA sequencing.,,pubmed:34486669,,HUB DB 009,GSM4635175,,tissue:Epicardial cells of the Zebrafish heart ventricle|line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,HUB DB 009,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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 order: 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 Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"". Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the Ensembl ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al. 2014 Cell Supplementary files format and content: *.TranscriptCounts.tsv: Tab delimited read count matrices in which rows correspond to genes and columns to single cells. Supplementary files format and content: cel seq2 barcodes.csv: Comma separated values",Epicardial cells of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgtcf21:mCherry cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,,line:Tgtcf21:mCherry|genotype/variation:WT|treatment:Cryoinjured heart|Stage:7dpi|cell type:Epicardial cells of adult heart ventricle,GSM4635175,GSM4635175: HUB DB 009; Danio rerio; RNA Seq,GSM4635175,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina TruSeq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for library prep Hashimony et al.  2016.,GEO Accession:GSM4635175,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP268691,,,HUB-DB-009_H3HCLBGXC_S1_L004_R1_001.fastq.gz HUB-DB-009_H3HCLBGXC_S1_L004_R2_001.fastq.gz,fastq fastq,872389848.0,10144068.0,GSM4635175 r4,0:26 1:60,A:211449890;C:164472082;G:170979230;T:325419371;N:69275,26,60,,,211449890,164472082,170979230,325419371,69275,SRX8610200,SRS6899878,SRA1090808,GEO,Hubrecht,2,0.10082,0.81569,0.09542,0.29303,0.99226,0.84033,0.65927,0.52879,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2020-06-24,Adult,Adult,Heart,Cardiovascular System
62867,SRR13426641,SRX9841732,SRS8023820,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 005,GSM5017826,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,HUB DB 005,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,GSM5017826,GSM5017826: HUB DB 005; Danio rerio; RNA Seq,GSM5017826,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017826,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,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,GSM5017826 r1,0:26 1:60,A:213590554;C:148614157;G:163804315;T:279996916;N:172592,26,60,,,213590554,148614157,163804315,279996916,172592,SRX9841732,SRS8023820,SRA1183369,GEO,FLI,2,0.10779,0.7922,0.10106,0.39356,0.99281,0.93701,0.66257,0.39639,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62868,SRR13426642,SRX9841732,SRS8023820,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 005,GSM5017826,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,HUB DB 005,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,GSM5017826,GSM5017826: HUB DB 005; Danio rerio; RNA Seq,GSM5017826,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017826,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,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,GSM5017826 r2,0:26 1:60,A:227213153;C:160851586;G:182364146;T:303951184;N:214217,26,60,,,227213153,160851586,182364146,303951184,214217,SRX9841732,SRS8023820,SRA1183369,GEO,FLI,2,0.11067,0.8032,0.10412,0.40169,0.9931,0.93332,0.65468,0.40908,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62869,SRR13426643,SRX9841732,SRS8023820,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 005,GSM5017826,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,HUB DB 005,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,GSM5017826,GSM5017826: HUB DB 005; Danio rerio; RNA Seq,GSM5017826,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017826,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,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,GSM5017826 r3,0:26 1:60,A:220300204;C:153061412;G:168938657;T:289375449;N:160138,26,60,,,220300204,153061412,168938657,289375449,160138,SRX9841732,SRS8023820,SRA1183369,GEO,FLI,2,0.10982,0.78672,0.10334,0.39196,0.99297,0.93675,0.64735,0.36252,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62870,SRR13426644,SRX9841732,SRS8023820,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 005,GSM5017826,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,HUB DB 005,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,GSM5017826,GSM5017826: HUB DB 005; Danio rerio; RNA Seq,GSM5017826,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017826,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,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,GSM5017826 r4,0:26 1:60,A:182418113;C:126757471;G:143869511;T:239393143;N:134898,26,60,,,182418113,126757471,143869511,239393143,134898,SRX9841732,SRS8023820,SRA1183369,GEO,FLI,2,0.10828,0.81367,0.10186,0.40356,0.99316,0.94018,0.65073,0.40086,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62871,SRR13426637,SRX9841731,SRS8023819,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 001,GSM5017825,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,HUB DB 001,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,GSM5017825,GSM5017825: HUB DB 001; Danio rerio; RNA Seq,GSM5017825,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017825,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,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,GSM5017825 r1,0:26 1:60,A:125045012;C:89627491;G:85413855;T:171466861;N:149815,26,60,,,125045012,89627491,85413855,171466861,149815,SRX9841731,SRS8023819,SRA1183369,GEO,FLI,2,0.10907,0.67995,0.10221,0.30484,0.99127,0.94229,0.63864,0.4574,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62872,SRR13426638,SRX9841731,SRS8023819,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 001,GSM5017825,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,HUB DB 001,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,GSM5017825,GSM5017825: HUB DB 001; Danio rerio; RNA Seq,GSM5017825,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017825,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,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,GSM5017825 r2,0:26 1:60,A:131516821;C:92202683;G:88685608;T:176824985;N:142841,26,60,,,131516821,92202683,88685608,176824985,142841,SRX9841731,SRS8023819,SRA1183369,GEO,FLI,2,0.11044,0.6808,0.10316,0.30432,0.99121,0.94868,0.59663,0.46502,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62873,SRR13426639,SRX9841731,SRS8023819,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 001,GSM5017825,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,HUB DB 001,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,GSM5017825,GSM5017825: HUB DB 001; Danio rerio; RNA Seq,GSM5017825,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017825,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,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,GSM5017825 r3,0:26 1:60,A:108841476;C:77418215;G:73171345;T:148203998;N:100254,26,60,,,108841476,77418215,73171345,148203998,100254,SRX9841731,SRS8023819,SRA1183369,GEO,FLI,2,0.10885,0.6707,0.10183,0.29574,0.99137,0.94702,0.66157,0.42386,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62874,SRR13426640,SRX9841731,SRS8023819,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 001,GSM5017825,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,HUB DB 001,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,GSM5017825,GSM5017825: HUB DB 001; Danio rerio; RNA Seq,GSM5017825,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017825,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,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,GSM5017825 r4,0:26 1:60,A:135189083;C:94908231;G:92431583;T:182885125;N:125282,26,60,,,135189083,94908231,92431583,182885125,125282,SRX9841731,SRS8023819,SRA1183369,GEO,FLI,2,0.10991,0.68593,0.10302,0.30489,0.99135,0.94799,0.66557,0.42206,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62875,SRR13426633,SRX9841730,SRS8023818,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 008,GSM5017831,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,HUB DB 008,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,GSM5017831,GSM5017831: HUB DB 008; Danio rerio; RNA Seq,GSM5017831,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017831,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,HUB-DB-008_HNWVVBGX9_S7_L001_R1_001.fastq.gz HUB-DB-008_HNWVVBGX9_S7_L001_R2_001.fastq.gz,fastq fastq,529790530.0,6160355.0,GSM5017831 r1,0:26 1:60,A:134254092;C:100685793;G:108463112;T:186279563;N:107970,26,60,,,134254092,100685793,108463112,186279563,107970,SRX9841730,SRS8023818,SRA1183369,GEO,FLI,2,0.11279,0.80911,0.10456,0.43276,0.99127,0.93927,0.65164,0.5415,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62876,SRR13426634,SRX9841730,SRS8023818,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 008,GSM5017831,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,HUB DB 008,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,GSM5017831,GSM5017831: HUB DB 008; Danio rerio; RNA Seq,GSM5017831,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017831,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,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,GSM5017831 r2,0:26 1:60,A:152137832;C:116026517;G:127735448;T:214967198;N:148127,26,60,,,152137832,116026517,127735448,214967198,148127,SRX9841730,SRS8023818,SRA1183369,GEO,FLI,2,0.11412,0.81784,0.1057,0.44203,0.99151,0.93421,0.59611,0.54448,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62877,SRR13426635,SRX9841730,SRS8023818,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 008,GSM5017831,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,HUB DB 008,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,GSM5017831,GSM5017831: HUB DB 008; Danio rerio; RNA Seq,GSM5017831,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017831,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,HUB-DB-008_HNWVVBGX9_S7_L003_R1_001.fastq.gz HUB-DB-008_HNWVVBGX9_S7_L003_R2_001.fastq.gz,fastq fastq,554981822.0,6453277.0,GSM5017831 r3,0:26 1:60,A:140664360;C:105281601;G:113575873;T:195359632;N:100356,26,60,,,140664360,105281601,113575873,195359632,100356,SRX9841730,SRS8023818,SRA1183369,GEO,FLI,2,0.11356,0.80646,0.10543,0.42991,0.99125,0.93996,0.67419,0.52863,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62878,SRR13426636,SRX9841730,SRS8023818,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 008,GSM5017831,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,HUB DB 008,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,GSM5017831,GSM5017831: HUB DB 008; Danio rerio; RNA Seq,GSM5017831,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017831,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,HUB-DB-008_HNWVVBGX9_S7_L004_R1_001.fastq.gz HUB-DB-008_HNWVVBGX9_S7_L004_R2_001.fastq.gz,fastq fastq,459861436.0,5347226.0,GSM5017831 r4,0:26 1:60,A:115949245;C:86913961;G:95720860;T:161187969;N:89401,26,60,,,115949245,86913961,95720860,161187969,89401,SRX9841730,SRS8023818,SRA1183369,GEO,FLI,2,0.11252,0.81111,0.10402,0.43407,0.99149,0.9403,0.64627,0.53769,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62879,SRR13426629,SRX9841729,SRS8023817,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 007,GSM5017830,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,HUB DB 007,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,GSM5017830,GSM5017830: HUB DB 007; Danio rerio; RNA Seq,GSM5017830,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017830,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,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,GSM5017830 r1,0:26 1:60,A:162038298;C:107975394;G:118251259;T:195669218;N:125285,26,60,,,162038298,107975394,118251259,195669218,125285,SRX9841729,SRS8023817,SRA1183369,GEO,FLI,2,0.08872,0.68675,0.08343,0.37824,0.99344,0.94957,0.6145,0.42826,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62880,SRR13426630,SRX9841729,SRS8023817,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 007,GSM5017830,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,HUB DB 007,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,GSM5017830,GSM5017830: HUB DB 007; Danio rerio; RNA Seq,GSM5017830,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017830,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,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,GSM5017830 r2,0:26 1:60,A:174443468;C:118438230;G:132604485;T:215721538;N:151727,26,60,,,174443468,118438230,132604485,215721538,151727,SRX9841729,SRS8023817,SRA1183369,GEO,FLI,2,0.09275,0.71424,0.08707,0.39397,0.99322,0.94582,0.56015,0.46192,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62881,SRR13426631,SRX9841729,SRS8023817,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 007,GSM5017830,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,HUB DB 007,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,GSM5017830,GSM5017830: HUB DB 007; Danio rerio; RNA Seq,GSM5017830,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017830,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,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,GSM5017830 r3,0:26 1:60,A:169007241;C:112556048;G:123345017;T:204831635;N:117105,26,60,,,169007241,112556048,123345017,204831635,117105,SRX9841729,SRS8023817,SRA1183369,GEO,FLI,2,0.09057,0.68247,0.08528,0.37739,0.99364,0.95144,0.57861,0.44968,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62882,SRR13426632,SRX9841729,SRS8023817,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 007,GSM5017830,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,HUB DB 007,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,GSM5017830,GSM5017830: HUB DB 007; Danio rerio; RNA Seq,GSM5017830,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017830,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,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,GSM5017830 r4,0:26 1:60,A:142060859;C:94579961;G:106100208;T:171916257;N:102681,26,60,,,142060859,94579961,106100208,171916257,102681,SRX9841729,SRS8023817,SRA1183369,GEO,FLI,2,0.08962,0.71759,0.08423,0.39506,0.99332,0.95187,0.54385,0.46164,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62883,SRR13426625,SRX9841728,SRS8023815,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 004,GSM5017829,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,HUB DB 004,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,GSM5017829,GSM5017829: HUB DB 004; Danio rerio; RNA Seq,GSM5017829,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017829,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,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,GSM5017829 r1,0:26 1:60,A:94538754;C:69024492;G:68361658;T:132108181;N:114651,26,60,,,94538754,69024492,68361658,132108181,114651,SRX9841728,SRS8023815,SRA1183369,GEO,FLI,2,0.11557,0.78274,0.10643,0.24244,0.98894,0.92723,0.57907,0.48282,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62884,SRR13426626,SRX9841728,SRS8023815,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 004,GSM5017829,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,HUB DB 004,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,GSM5017829,GSM5017829: HUB DB 004; Danio rerio; RNA Seq,GSM5017829,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017829,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,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,GSM5017829 r2,0:26 1:60,A:99999342;C:71104204;G:70005970;T:136434888;N:108858,26,60,,,99999342,71104204,70005970,136434888,108858,SRX9841728,SRS8023815,SRA1183369,GEO,FLI,2,0.11403,0.78001,0.10527,0.24048,0.98971,0.93622,0.60354,0.43409,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62885,SRR13426627,SRX9841728,SRS8023815,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 004,GSM5017829,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,HUB DB 004,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,GSM5017829,GSM5017829: HUB DB 004; Danio rerio; RNA Seq,GSM5017829,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017829,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,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,GSM5017829 r3,0:26 1:60,A:80261116;C:58220837;G:57196503;T:111195958;N:73174,26,60,,,80261116,58220837,57196503,111195958,73174,SRX9841728,SRS8023815,SRA1183369,GEO,FLI,2,0.1114,0.76714,0.1024,0.23795,0.98914,0.93298,0.62672,0.47747,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62886,SRR13426628,SRX9841728,SRS8023815,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 004,GSM5017829,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,HUB DB 004,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,GSM5017829,GSM5017829: HUB DB 004; Danio rerio; RNA Seq,GSM5017829,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017829,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,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,GSM5017829 r4,0:26 1:60,A:102486709;C:73105388;G:73019179;T:140769931;N:91207,26,60,,,102486709,73105388,73019179,140769931,91207,SRX9841728,SRS8023815,SRA1183369,GEO,FLI,2,0.11501,0.7831,0.10673,0.24184,0.98922,0.93314,0.62652,0.4358,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62887,SRR13426621,SRX9841727,SRS8023816,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 003,GSM5017828,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,HUB DB 003,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,GSM5017828,GSM5017828: HUB DB 003; Danio rerio; RNA Seq,GSM5017828,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017828,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,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,GSM5017828 r1,0:26 1:60,A:102130758;C:71032768;G:73641442;T:134437630;N:123026,26,60,,,102130758,71032768,73641442,134437630,123026,SRX9841727,SRS8023816,SRA1183369,GEO,FLI,2,0.1005,0.72438,0.09204,0.25516,0.98916,0.92999,0.5282,0.51145,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62888,SRR13426622,SRX9841727,SRS8023816,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 003,GSM5017828,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,HUB DB 003,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,GSM5017828,GSM5017828: HUB DB 003; Danio rerio; RNA Seq,GSM5017828,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017828,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,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,GSM5017828 r2,0:26 1:60,A:109307778;C:73934198;G:76916762;T:140249156;N:117326,26,60,,,109307778,73934198,76916762,140249156,117326,SRX9841727,SRS8023816,SRA1183369,GEO,FLI,2,0.09923,0.71599,0.0907,0.25109,0.98942,0.93939,0.54426,0.5102,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62889,SRR13426623,SRX9841727,SRS8023816,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 003,GSM5017828,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,HUB DB 003,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,GSM5017828,GSM5017828: HUB DB 003; Danio rerio; RNA Seq,GSM5017828,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017828,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,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,GSM5017828 r3,0:26 1:60,A:91716565;C:63676514;G:65563102;T:120323617;N:84216,26,60,,,91716565,63676514,65563102,120323617,84216,SRX9841727,SRS8023816,SRA1183369,GEO,FLI,2,0.09825,0.70792,0.09006,0.2519,0.98914,0.93799,0.50626,0.49668,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62890,SRR13426624,SRX9841727,SRS8023816,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 003,GSM5017828,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,HUB DB 003,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle,GSM5017828,GSM5017828: HUB DB 003; Danio rerio; RNA Seq,GSM5017828,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017828,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,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,GSM5017828 r4,0:26 1:60,A:112224009;C:76213738;G:80259829;T:145201785;N:101371,26,60,,,112224009,76213738,80259829,145201785,101371,SRX9841727,SRS8023816,SRA1183369,GEO,FLI,2,0.10103,0.71991,0.09307,0.25283,0.98932,0.93683,0.53111,0.51224,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62891,SRR13426620,SRX9841726,SRS8023814,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 006,GSM5017827,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,HUB DB 006,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,GSM5017827,GSM5017827: HUB DB 006; Danio rerio; RNA Seq,GSM5017827,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017827,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,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,GSM5017827 r4,0:26 1:60,A:205538880;C:148510556;G:161196381;T:282964175;N:160774,26,60,,,205538880,148510556,161196381,282964175,160774,SRX9841726,SRS8023814,SRA1183369,GEO,FLI,2,0.11016,0.87019,0.10207,0.43584,0.99233,0.93332,0.56371,0.44363,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62892,SRR13426645,SRX9841726,SRS8023814,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 006,GSM5017827,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,HUB DB 006,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,GSM5017827,GSM5017827: HUB DB 006; Danio rerio; RNA Seq,GSM5017827,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017827,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,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,GSM5017827 r1,0:26 1:60,A:240334465;C:174255952;G:184260587;T:330943403;N:205121,26,60,,,240334465,174255952,184260587,330943403,205121,SRX9841726,SRS8023814,SRA1183369,GEO,FLI,2,0.11112,0.87401,0.10296,0.43854,0.99176,0.9303,0.62237,0.4398,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62893,SRR13426646,SRX9841726,SRS8023814,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 006,GSM5017827,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,HUB DB 006,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,GSM5017827,GSM5017827: HUB DB 006; Danio rerio; RNA Seq,GSM5017827,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017827,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,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,GSM5017827 r2,0:26 1:60,A:251121714;C:184449811;G:201317783;T:350692225;N:243363,26,60,,,251121714,184449811,201317783,350692225,243363,SRX9841726,SRS8023814,SRA1183369,GEO,FLI,2,0.1127,0.87874,0.10425,0.44506,0.99172,0.92512,0.62378,0.45501,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
62894,SRR13426647,SRX9841726,SRS8023814,SRP301573,PRJNA691756,Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential,GSE164729,Transcriptome Analysis,Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.,,,,HUB DB 006,GSM5017827,,source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,HUB DB 006,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 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. Sample 3 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 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.",Cardiomyocytes of the Zebrafish heart ventricle,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine;hmga1a+/+|tissue:Adult zebrafish ventricle,GSM5017827,GSM5017827: HUB DB 006; Danio rerio; RNA Seq,GSM5017827,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM5017827,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP301573,,,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,GSM5017827 r3,0:26 1:60,A:247983556;C:179564753;G:190342582;T:341858456;N:183685,26,60,,,247983556,179564753,190342582,341858456,183685,SRX9841726,SRS8023814,SRA1183369,GEO,FLI,2,0.11184,0.87155,0.10357,0.43949,0.99176,0.93028,0.65392,0.44113,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Germany,2021-01-13,Adult,Adult,Heart,Cardiovascular System
69488,SRR18745494,SRX14845536,SRS12600438,SRP370089,PRJNA826497,Stage  and cell type specific requirements of ikzf1 during haematopoietic differentiation in zebrafish,GSE200756,Transcriptome Analysis,The zinc finger transcription factor Ikaros1 Ikzf1 is required for lymphoid development in mammals. It is characterized by the presence of four zinc fingers in its DNA binding domain and two zinc fingers in the C terminal protein interaction module. Here  we describe the phenotypes of zebrafish homozygous for two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain. Our results indicate that an intact ikzf1 gene is required for larval T cell development  whereas low levels of adult lymphoid development recover in the mutants. By contrast  the mutants exhibit a signature of increased myelopoiesis at larval and adult stages. Of note  both mutants stimulate erythroid differentiation in larvae  indicating that the C terminal zinc fingers negatively regulate the extent of red blood cell production. An unexpected differential effect of the two mutants on adult erythropoiesis suggests a direct requirement of an intact DNA binding domain for entry of progenitors into the red blood cell lineage. Collectively  our results reinforce the biological differences between larval and adult haematopoiesis  indicate a stage specific function of ikzf1 in regulating the hierarchical bifurcations of differentiation  and assign distinct functions to the DNA binding domain and the C terminal zinc fingers. Overall design: Single cell RNA sequencing was performed to examine the cellular heterogeneity of whole kidney marrow WKM cells in wild type and two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain.,,pubmed:36496511,,WT P2 8,GSM6043281,,source name:whole kidney marrow WKM|tissue:whole kidney marrow WKM|age:3 month|genotype/variation:Wildtype WKM cells,WT P2 8,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57 207 isoforms derived from 57 207 gene loci with 57 114 isoforms mapping to fully annotated chromosomes 1 to 19  X  Y  M. All isoforms of the same gene were merged to a single gene locus. Furthermore  gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34 111 gene groups. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Assembly: ENCODE VM9 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,whole kidney marrow WKM,No Treatment was performed.,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,Zebrafish strains were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics.,tissue:whole kidney marrow WKM|age:3 month|genotype/variation:Wildtype WKM cells,GSM6043281,GSM6043281: WT P2 8; Danio rerio; RNA Seq,GSM6043281 r1,GSM6043281,1,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP370089,,,WT_P2_8_R1.fastq.gz WT_P2_8_R2.fastq.gz,fastq fastq,1632541600.0,16325416.0,GSM6043281 r1,0:30 1:70,A:404066016;C:283061574;G:293117581;T:647752220;N:4544209,30,70,,,404066016,283061574,293117581,647752220,4544209,SRX14845536,SRS12600438,SRA1403848,"Sagar, Department of Internal Medicine II, University Medical Center Freiburg","Sagar, Department of Internal Medicine II, University Medical Center Freiburg",2,0.42751,0.85533,0.39919,0.29078,0.99151,0.83887,0.87048,0.66927,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2022-04-13,Adult,Adult,Kidney,Renal System
69489,SRR18745495,SRX14845535,SRS12600437,SRP370089,PRJNA826497,Stage  and cell type specific requirements of ikzf1 during haematopoietic differentiation in zebrafish,GSE200756,Transcriptome Analysis,The zinc finger transcription factor Ikaros1 Ikzf1 is required for lymphoid development in mammals. It is characterized by the presence of four zinc fingers in its DNA binding domain and two zinc fingers in the C terminal protein interaction module. Here  we describe the phenotypes of zebrafish homozygous for two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain. Our results indicate that an intact ikzf1 gene is required for larval T cell development  whereas low levels of adult lymphoid development recover in the mutants. By contrast  the mutants exhibit a signature of increased myelopoiesis at larval and adult stages. Of note  both mutants stimulate erythroid differentiation in larvae  indicating that the C terminal zinc fingers negatively regulate the extent of red blood cell production. An unexpected differential effect of the two mutants on adult erythropoiesis suggests a direct requirement of an intact DNA binding domain for entry of progenitors into the red blood cell lineage. Collectively  our results reinforce the biological differences between larval and adult haematopoiesis  indicate a stage specific function of ikzf1 in regulating the hierarchical bifurcations of differentiation  and assign distinct functions to the DNA binding domain and the C terminal zinc fingers. Overall design: Single cell RNA sequencing was performed to examine the cellular heterogeneity of whole kidney marrow WKM cells in wild type and two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain.,,pubmed:36496511,,WT P2 7,GSM6043280,,source name:whole kidney marrow WKM|tissue:whole kidney marrow WKM|age:3 month|genotype/variation:Wildtype WKM cells,WT P2 7,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57 207 isoforms derived from 57 207 gene loci with 57 114 isoforms mapping to fully annotated chromosomes 1 to 19  X  Y  M. All isoforms of the same gene were merged to a single gene locus. Furthermore  gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34 111 gene groups. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Assembly: ENCODE VM9 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,whole kidney marrow WKM,No Treatment was performed.,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,Zebrafish strains were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics.,tissue:whole kidney marrow WKM|age:3 month|genotype/variation:Wildtype WKM cells,GSM6043280,GSM6043280: WT P2 7; Danio rerio; RNA Seq,GSM6043280 r1,GSM6043280,1,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP370089,,,WT_P2_7_R1.fastq.gz WT_P2_7_R2.fastq.gz,fastq fastq,1623632100.0,16236321.0,GSM6043280 r1,0:30 1:70,A:419230631;C:276740241;G:284553367;T:638637455;N:4470406,30,70,,,419230631,276740241,284553367,638637455,4470406,SRX14845535,SRS12600437,SRA1403848,"Sagar, Department of Internal Medicine II, University Medical Center Freiburg","Sagar, Department of Internal Medicine II, University Medical Center Freiburg",2,0.49448,0.82629,0.45692,0.39381,0.99107,0.82223,0.81813,0.64627,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2022-04-13,Adult,Adult,Kidney,Renal System
69490,SRR18745496,SRX14845534,SRS12600436,SRP370089,PRJNA826497,Stage  and cell type specific requirements of ikzf1 during haematopoietic differentiation in zebrafish,GSE200756,Transcriptome Analysis,The zinc finger transcription factor Ikaros1 Ikzf1 is required for lymphoid development in mammals. It is characterized by the presence of four zinc fingers in its DNA binding domain and two zinc fingers in the C terminal protein interaction module. Here  we describe the phenotypes of zebrafish homozygous for two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain. Our results indicate that an intact ikzf1 gene is required for larval T cell development  whereas low levels of adult lymphoid development recover in the mutants. By contrast  the mutants exhibit a signature of increased myelopoiesis at larval and adult stages. Of note  both mutants stimulate erythroid differentiation in larvae  indicating that the C terminal zinc fingers negatively regulate the extent of red blood cell production. An unexpected differential effect of the two mutants on adult erythropoiesis suggests a direct requirement of an intact DNA binding domain for entry of progenitors into the red blood cell lineage. Collectively  our results reinforce the biological differences between larval and adult haematopoiesis  indicate a stage specific function of ikzf1 in regulating the hierarchical bifurcations of differentiation  and assign distinct functions to the DNA binding domain and the C terminal zinc fingers. Overall design: Single cell RNA sequencing was performed to examine the cellular heterogeneity of whole kidney marrow WKM cells in wild type and two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain.,,pubmed:36496511,,WT P2 6,GSM6043279,,source name:whole kidney marrow WKM|tissue:whole kidney marrow WKM|age:3 month|genotype/variation:Wildtype WKM cells,WT P2 6,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57 207 isoforms derived from 57 207 gene loci with 57 114 isoforms mapping to fully annotated chromosomes 1 to 19  X  Y  M. All isoforms of the same gene were merged to a single gene locus. Furthermore  gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34 111 gene groups. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Assembly: ENCODE VM9 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,whole kidney marrow WKM,No Treatment was performed.,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,Zebrafish strains were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics.,tissue:whole kidney marrow WKM|age:3 month|genotype/variation:Wildtype WKM cells,GSM6043279,GSM6043279: WT P2 6; Danio rerio; RNA Seq,GSM6043279 r1,GSM6043279,1,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP370089,,,WT_P2_6_R1.fastq.gz WT_P2_6_R2.fastq.gz,fastq fastq,1667147800.0,16671478.0,GSM6043279 r1,0:30 1:70,A:426337135;C:282627807;G:298573332;T:655007098;N:4602428,30,70,,,426337135,282627807,298573332,655007098,4602428,SRX14845534,SRS12600436,SRA1403848,"Sagar, Department of Internal Medicine II, University Medical Center Freiburg","Sagar, Department of Internal Medicine II, University Medical Center Freiburg",2,0.44775,0.83006,0.41422,0.30445,0.99249,0.83575,0.71109,0.66532,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2022-04-13,Adult,Adult,Kidney,Renal System
69491,SRR18745500,SRX14845533,SRS12600435,SRP370089,PRJNA826497,Stage  and cell type specific requirements of ikzf1 during haematopoietic differentiation in zebrafish,GSE200756,Transcriptome Analysis,The zinc finger transcription factor Ikaros1 Ikzf1 is required for lymphoid development in mammals. It is characterized by the presence of four zinc fingers in its DNA binding domain and two zinc fingers in the C terminal protein interaction module. Here  we describe the phenotypes of zebrafish homozygous for two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain. Our results indicate that an intact ikzf1 gene is required for larval T cell development  whereas low levels of adult lymphoid development recover in the mutants. By contrast  the mutants exhibit a signature of increased myelopoiesis at larval and adult stages. Of note  both mutants stimulate erythroid differentiation in larvae  indicating that the C terminal zinc fingers negatively regulate the extent of red blood cell production. An unexpected differential effect of the two mutants on adult erythropoiesis suggests a direct requirement of an intact DNA binding domain for entry of progenitors into the red blood cell lineage. Collectively  our results reinforce the biological differences between larval and adult haematopoiesis  indicate a stage specific function of ikzf1 in regulating the hierarchical bifurcations of differentiation  and assign distinct functions to the DNA binding domain and the C terminal zinc fingers. Overall design: Single cell RNA sequencing was performed to examine the cellular heterogeneity of whole kidney marrow WKM cells in wild type and two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain.,,pubmed:36496511,,WT P2 5,GSM6043278,,source name:whole kidney marrow WKM|tissue:whole kidney marrow WKM|age:3 month|genotype/variation:Wildtype WKM cells,WT P2 5,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57 207 isoforms derived from 57 207 gene loci with 57 114 isoforms mapping to fully annotated chromosomes 1 to 19  X  Y  M. All isoforms of the same gene were merged to a single gene locus. Furthermore  gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34 111 gene groups. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Assembly: ENCODE VM9 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,whole kidney marrow WKM,No Treatment was performed.,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,Zebrafish strains were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics.,tissue:whole kidney marrow WKM|age:3 month|genotype/variation:Wildtype WKM cells,GSM6043278,GSM6043278: WT P2 5; Danio rerio; RNA Seq,GSM6043278 r1,GSM6043278,1,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP370089,,,WT_P2_5_R1.fastq.gz WT_P2_5_R2.fastq.gz,fastq fastq,1696686500.0,16966865.0,GSM6043278 r1,0:30 1:70,A:430216944;C:290331313;G:298182623;T:673268789;N:4686831,30,70,,,430216944,290331313,298182623,673268789,4686831,SRX14845533,SRS12600435,SRA1403848,"Sagar, Department of Internal Medicine II, University Medical Center Freiburg","Sagar, Department of Internal Medicine II, University Medical Center Freiburg",2,0.44807,0.83604,0.43395,0.37042,0.99123,0.81375,0.65888,0.6396,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2022-04-13,Adult,Adult,Kidney,Renal System
69492,SRR18745497,SRX14845532,SRS12600434,SRP370089,PRJNA826497,Stage  and cell type specific requirements of ikzf1 during haematopoietic differentiation in zebrafish,GSE200756,Transcriptome Analysis,The zinc finger transcription factor Ikaros1 Ikzf1 is required for lymphoid development in mammals. It is characterized by the presence of four zinc fingers in its DNA binding domain and two zinc fingers in the C terminal protein interaction module. Here  we describe the phenotypes of zebrafish homozygous for two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain. Our results indicate that an intact ikzf1 gene is required for larval T cell development  whereas low levels of adult lymphoid development recover in the mutants. By contrast  the mutants exhibit a signature of increased myelopoiesis at larval and adult stages. Of note  both mutants stimulate erythroid differentiation in larvae  indicating that the C terminal zinc fingers negatively regulate the extent of red blood cell production. An unexpected differential effect of the two mutants on adult erythropoiesis suggests a direct requirement of an intact DNA binding domain for entry of progenitors into the red blood cell lineage. Collectively  our results reinforce the biological differences between larval and adult haematopoiesis  indicate a stage specific function of ikzf1 in regulating the hierarchical bifurcations of differentiation  and assign distinct functions to the DNA binding domain and the C terminal zinc fingers. Overall design: Single cell RNA sequencing was performed to examine the cellular heterogeneity of whole kidney marrow WKM cells in wild type and two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain.,,pubmed:36496511,,WT P1 4,GSM6043277,,source name:whole kidney marrow WKM|tissue:whole kidney marrow WKM|age:3 month|genotype/variation:Wildtype WKM cells,WT P1 4,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57 207 isoforms derived from 57 207 gene loci with 57 114 isoforms mapping to fully annotated chromosomes 1 to 19  X  Y  M. All isoforms of the same gene were merged to a single gene locus. Furthermore  gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34 111 gene groups. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Assembly: ENCODE VM9 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,whole kidney marrow WKM,No Treatment was performed.,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,Zebrafish strains were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics.,tissue:whole kidney marrow WKM|age:3 month|genotype/variation:Wildtype WKM cells,GSM6043277,GSM6043277: WT P1 4; Danio rerio; RNA Seq,GSM6043277 r1,GSM6043277,1,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP370089,,,WT_P1_4_R1.fastq.gz WT_P1_4_R2.fastq.gz,fastq fastq,1021033300.0,10210333.0,GSM6043277 r1,0:30 1:70,A:262045012;C:177588517;G:180917158;T:397662980;N:2819633,30,70,,,262045012,177588517,180917158,397662980,2819633,SRX14845532,SRS12600434,SRA1403848,"Sagar, Department of Internal Medicine II, University Medical Center Freiburg","Sagar, Department of Internal Medicine II, University Medical Center Freiburg",2,0.3422,0.82101,0.32257,0.39349,0.99285,0.84875,0.74599,0.6683,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2022-04-13,Adult,Adult,Kidney,Renal System
69493,SRR18745498,SRX14845531,SRS12600433,SRP370089,PRJNA826497,Stage  and cell type specific requirements of ikzf1 during haematopoietic differentiation in zebrafish,GSE200756,Transcriptome Analysis,The zinc finger transcription factor Ikaros1 Ikzf1 is required for lymphoid development in mammals. It is characterized by the presence of four zinc fingers in its DNA binding domain and two zinc fingers in the C terminal protein interaction module. Here  we describe the phenotypes of zebrafish homozygous for two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain. Our results indicate that an intact ikzf1 gene is required for larval T cell development  whereas low levels of adult lymphoid development recover in the mutants. By contrast  the mutants exhibit a signature of increased myelopoiesis at larval and adult stages. Of note  both mutants stimulate erythroid differentiation in larvae  indicating that the C terminal zinc fingers negatively regulate the extent of red blood cell production. An unexpected differential effect of the two mutants on adult erythropoiesis suggests a direct requirement of an intact DNA binding domain for entry of progenitors into the red blood cell lineage. Collectively  our results reinforce the biological differences between larval and adult haematopoiesis  indicate a stage specific function of ikzf1 in regulating the hierarchical bifurcations of differentiation  and assign distinct functions to the DNA binding domain and the C terminal zinc fingers. Overall design: Single cell RNA sequencing was performed to examine the cellular heterogeneity of whole kidney marrow WKM cells in wild type and two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain.,,pubmed:36496511,,WT P1 3,GSM6043276,,source name:whole kidney marrow WKM|tissue:whole kidney marrow WKM|age:3 month|genotype/variation:Wildtype WKM cells,WT P1 3,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57 207 isoforms derived from 57 207 gene loci with 57 114 isoforms mapping to fully annotated chromosomes 1 to 19  X  Y  M. All isoforms of the same gene were merged to a single gene locus. Furthermore  gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34 111 gene groups. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Assembly: ENCODE VM9 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,whole kidney marrow WKM,No Treatment was performed.,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,Zebrafish strains were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics.,tissue:whole kidney marrow WKM|age:3 month|genotype/variation:Wildtype WKM cells,GSM6043276,GSM6043276: WT P1 3; Danio rerio; RNA Seq,GSM6043276 r1,GSM6043276,1,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP370089,,,WT_P1_3_R1.fastq.gz WT_P1_3_R2.fastq.gz,fastq fastq,1336723700.0,13367237.0,GSM6043276 r1,0:30 1:70,A:344059610;C:231839361;G:240653366;T:516482850;N:3688513,30,70,,,344059610,231839361,240653366,516482850,3688513,SRX14845531,SRS12600433,SRA1403848,"Sagar, Department of Internal Medicine II, University Medical Center Freiburg","Sagar, Department of Internal Medicine II, University Medical Center Freiburg",2,0.50066,0.83353,0.47888,0.33553,0.99095,0.83798,0.53243,0.64931,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2022-04-13,Adult,Adult,Kidney,Renal System
69494,SRR18745499,SRX14845530,SRS12600432,SRP370089,PRJNA826497,Stage  and cell type specific requirements of ikzf1 during haematopoietic differentiation in zebrafish,GSE200756,Transcriptome Analysis,The zinc finger transcription factor Ikaros1 Ikzf1 is required for lymphoid development in mammals. It is characterized by the presence of four zinc fingers in its DNA binding domain and two zinc fingers in the C terminal protein interaction module. Here  we describe the phenotypes of zebrafish homozygous for two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain. Our results indicate that an intact ikzf1 gene is required for larval T cell development  whereas low levels of adult lymphoid development recover in the mutants. By contrast  the mutants exhibit a signature of increased myelopoiesis at larval and adult stages. Of note  both mutants stimulate erythroid differentiation in larvae  indicating that the C terminal zinc fingers negatively regulate the extent of red blood cell production. An unexpected differential effect of the two mutants on adult erythropoiesis suggests a direct requirement of an intact DNA binding domain for entry of progenitors into the red blood cell lineage. Collectively  our results reinforce the biological differences between larval and adult haematopoiesis  indicate a stage specific function of ikzf1 in regulating the hierarchical bifurcations of differentiation  and assign distinct functions to the DNA binding domain and the C terminal zinc fingers. Overall design: Single cell RNA sequencing was performed to examine the cellular heterogeneity of whole kidney marrow WKM cells in wild type and two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain.,,pubmed:36496511,,WT P1 2,GSM6043275,,source name:whole kidney marrow WKM|tissue:whole kidney marrow WKM|age:3 month|genotype/variation:Wildtype WKM cells,WT P1 2,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57 207 isoforms derived from 57 207 gene loci with 57 114 isoforms mapping to fully annotated chromosomes 1 to 19  X  Y  M. All isoforms of the same gene were merged to a single gene locus. Furthermore  gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34 111 gene groups. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Assembly: ENCODE VM9 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,whole kidney marrow WKM,No Treatment was performed.,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,Zebrafish strains were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics.,tissue:whole kidney marrow WKM|age:3 month|genotype/variation:Wildtype WKM cells,GSM6043275,GSM6043275: WT P1 2; Danio rerio; RNA Seq,GSM6043275 r1,GSM6043275,1,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP370089,,,WT_P1_2_R1.fastq.gz WT_P1_2_R2.fastq.gz,fastq fastq,1393504300.0,13935043.0,GSM6043275 r1,0:30 1:70,A:362840491;C:240805875;G:241430489;T:544595841;N:3831604,30,70,,,362840491,240805875,241430489,544595841,3831604,SRX14845530,SRS12600432,SRA1403848,"Sagar, Department of Internal Medicine II, University Medical Center Freiburg","Sagar, Department of Internal Medicine II, University Medical Center Freiburg",2,0.45074,0.81078,0.43016,0.39084,0.99103,0.83276,0.77358,0.66059,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2022-04-13,Adult,Adult,Kidney,Renal System
69495,SRR18745501,SRX14845529,SRS12600431,SRP370089,PRJNA826497,Stage  and cell type specific requirements of ikzf1 during haematopoietic differentiation in zebrafish,GSE200756,Transcriptome Analysis,The zinc finger transcription factor Ikaros1 Ikzf1 is required for lymphoid development in mammals. It is characterized by the presence of four zinc fingers in its DNA binding domain and two zinc fingers in the C terminal protein interaction module. Here  we describe the phenotypes of zebrafish homozygous for two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain. Our results indicate that an intact ikzf1 gene is required for larval T cell development  whereas low levels of adult lymphoid development recover in the mutants. By contrast  the mutants exhibit a signature of increased myelopoiesis at larval and adult stages. Of note  both mutants stimulate erythroid differentiation in larvae  indicating that the C terminal zinc fingers negatively regulate the extent of red blood cell production. An unexpected differential effect of the two mutants on adult erythropoiesis suggests a direct requirement of an intact DNA binding domain for entry of progenitors into the red blood cell lineage. Collectively  our results reinforce the biological differences between larval and adult haematopoiesis  indicate a stage specific function of ikzf1 in regulating the hierarchical bifurcations of differentiation  and assign distinct functions to the DNA binding domain and the C terminal zinc fingers. Overall design: Single cell RNA sequencing was performed to examine the cellular heterogeneity of whole kidney marrow WKM cells in wild type and two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain.,,pubmed:36496511,,WT P1 1,GSM6043274,,source name:whole kidney marrow WKM|tissue:whole kidney marrow WKM|age:3 month|genotype/variation:Wildtype WKM cells,WT P1 1,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57 207 isoforms derived from 57 207 gene loci with 57 114 isoforms mapping to fully annotated chromosomes 1 to 19  X  Y  M. All isoforms of the same gene were merged to a single gene locus. Furthermore  gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34 111 gene groups. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Assembly: ENCODE VM9 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,whole kidney marrow WKM,No Treatment was performed.,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,Zebrafish strains were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics.,tissue:whole kidney marrow WKM|age:3 month|genotype/variation:Wildtype WKM cells,GSM6043274,GSM6043274: WT P1 1; Danio rerio; RNA Seq,GSM6043274 r1,GSM6043274,1,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP370089,,,WT_P1_1_R1.fastq.gz WT_P1_1_R2.fastq.gz,fastq fastq,1615231900.0,16152319.0,GSM6043274 r1,0:30 1:70,A:400583887;C:283106184;G:291933592;T:635127158;N:4481079,30,70,,,400583887,283106184,291933592,635127158,4481079,SRX14845529,SRS12600431,SRA1403848,"Sagar, Department of Internal Medicine II, University Medical Center Freiburg","Sagar, Department of Internal Medicine II, University Medical Center Freiburg",2,0.5555,0.8392,0.53202,0.3164,0.99123,0.828,0.84555,0.6639,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2022-04-13,Adult,Adult,Kidney,Renal System
69496,SRR18745502,SRX14845528,SRS12600430,SRP370089,PRJNA826497,Stage  and cell type specific requirements of ikzf1 during haematopoietic differentiation in zebrafish,GSE200756,Transcriptome Analysis,The zinc finger transcription factor Ikaros1 Ikzf1 is required for lymphoid development in mammals. It is characterized by the presence of four zinc fingers in its DNA binding domain and two zinc fingers in the C terminal protein interaction module. Here  we describe the phenotypes of zebrafish homozygous for two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain. Our results indicate that an intact ikzf1 gene is required for larval T cell development  whereas low levels of adult lymphoid development recover in the mutants. By contrast  the mutants exhibit a signature of increased myelopoiesis at larval and adult stages. Of note  both mutants stimulate erythroid differentiation in larvae  indicating that the C terminal zinc fingers negatively regulate the extent of red blood cell production. An unexpected differential effect of the two mutants on adult erythropoiesis suggests a direct requirement of an intact DNA binding domain for entry of progenitors into the red blood cell lineage. Collectively  our results reinforce the biological differences between larval and adult haematopoiesis  indicate a stage specific function of ikzf1 in regulating the hierarchical bifurcations of differentiation  and assign distinct functions to the DNA binding domain and the C terminal zinc fingers. Overall design: Single cell RNA sequencing was performed to examine the cellular heterogeneity of whole kidney marrow WKM cells in wild type and two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain.,,pubmed:36496511,,IT325 P2 4,GSM6043273,,source name:whole kidney marrow WKM|tissue:whole kidney marrow WKM|age:3 month|genotype/variation:IT325 Mutant WKM cells,IT325 P2 4,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57 207 isoforms derived from 57 207 gene loci with 57 114 isoforms mapping to fully annotated chromosomes 1 to 19  X  Y  M. All isoforms of the same gene were merged to a single gene locus. Furthermore  gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34 111 gene groups. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Assembly: ENCODE VM9 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,whole kidney marrow WKM,No Treatment was performed.,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,Zebrafish strains were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics.,tissue:whole kidney marrow WKM|age:3 month|genotype/variation:IT325 Mutant WKM cells,GSM6043273,GSM6043273: IT325 P2 4; Danio rerio; RNA Seq,GSM6043273 r1,GSM6043273,1,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP370089,,,IT325_P2_4_R1.fastq.gz IT325_P2_4_R2.fastq.gz,fastq fastq,1701241900.0,17012419.0,GSM6043273 r1,0:30 1:70,A:414457894;C:300146561;G:309526103;T:673629079;N:3482263,30,70,,,414457894,300146561,309526103,673629079,3482263,SRX14845528,SRS12600430,SRA1403848,"Sagar, Department of Internal Medicine II, University Medical Center Freiburg","Sagar, Department of Internal Medicine II, University Medical Center Freiburg",2,0.48001,0.84765,0.44847,0.29632,0.99082,0.81854,0.71944,0.65045,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2022-04-13,Adult,Adult,Kidney,Renal System
69497,SRR18745503,SRX14845527,SRS12600429,SRP370089,PRJNA826497,Stage  and cell type specific requirements of ikzf1 during haematopoietic differentiation in zebrafish,GSE200756,Transcriptome Analysis,The zinc finger transcription factor Ikaros1 Ikzf1 is required for lymphoid development in mammals. It is characterized by the presence of four zinc fingers in its DNA binding domain and two zinc fingers in the C terminal protein interaction module. Here  we describe the phenotypes of zebrafish homozygous for two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain. Our results indicate that an intact ikzf1 gene is required for larval T cell development  whereas low levels of adult lymphoid development recover in the mutants. By contrast  the mutants exhibit a signature of increased myelopoiesis at larval and adult stages. Of note  both mutants stimulate erythroid differentiation in larvae  indicating that the C terminal zinc fingers negatively regulate the extent of red blood cell production. An unexpected differential effect of the two mutants on adult erythropoiesis suggests a direct requirement of an intact DNA binding domain for entry of progenitors into the red blood cell lineage. Collectively  our results reinforce the biological differences between larval and adult haematopoiesis  indicate a stage specific function of ikzf1 in regulating the hierarchical bifurcations of differentiation  and assign distinct functions to the DNA binding domain and the C terminal zinc fingers. Overall design: Single cell RNA sequencing was performed to examine the cellular heterogeneity of whole kidney marrow WKM cells in wild type and two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain.,,pubmed:36496511,,IT325 P2 3,GSM6043272,,source name:whole kidney marrow WKM|tissue:whole kidney marrow WKM|age:3 month|genotype/variation:IT325 Mutant WKM cells,IT325 P2 3,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57 207 isoforms derived from 57 207 gene loci with 57 114 isoforms mapping to fully annotated chromosomes 1 to 19  X  Y  M. All isoforms of the same gene were merged to a single gene locus. Furthermore  gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34 111 gene groups. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Assembly: ENCODE VM9 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,whole kidney marrow WKM,No Treatment was performed.,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,Zebrafish strains were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics.,tissue:whole kidney marrow WKM|age:3 month|genotype/variation:IT325 Mutant WKM cells,GSM6043272,GSM6043272: IT325 P2 3; Danio rerio; RNA Seq,GSM6043272 r1,GSM6043272,1,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP370089,,,IT325_P2_3_R1.fastq.gz IT325_P2_3_R2.fastq.gz,fastq fastq,1960417900.0,19604179.0,GSM6043272 r1,0:30 1:70,A:484747999;C:347404082;G:352634267;T:771615308;N:4016244,30,70,,,484747999,347404082,352634267,771615308,4016244,SRX14845527,SRS12600429,SRA1403848,"Sagar, Department of Internal Medicine II, University Medical Center Freiburg","Sagar, Department of Internal Medicine II, University Medical Center Freiburg",2,0.54892,0.85274,0.5191,0.27943,0.99192,0.81824,0.84214,0.66385,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2022-04-13,Adult,Adult,Kidney,Renal System
69498,SRR18745504,SRX14845526,SRS12600428,SRP370089,PRJNA826497,Stage  and cell type specific requirements of ikzf1 during haematopoietic differentiation in zebrafish,GSE200756,Transcriptome Analysis,The zinc finger transcription factor Ikaros1 Ikzf1 is required for lymphoid development in mammals. It is characterized by the presence of four zinc fingers in its DNA binding domain and two zinc fingers in the C terminal protein interaction module. Here  we describe the phenotypes of zebrafish homozygous for two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain. Our results indicate that an intact ikzf1 gene is required for larval T cell development  whereas low levels of adult lymphoid development recover in the mutants. By contrast  the mutants exhibit a signature of increased myelopoiesis at larval and adult stages. Of note  both mutants stimulate erythroid differentiation in larvae  indicating that the C terminal zinc fingers negatively regulate the extent of red blood cell production. An unexpected differential effect of the two mutants on adult erythropoiesis suggests a direct requirement of an intact DNA binding domain for entry of progenitors into the red blood cell lineage. Collectively  our results reinforce the biological differences between larval and adult haematopoiesis  indicate a stage specific function of ikzf1 in regulating the hierarchical bifurcations of differentiation  and assign distinct functions to the DNA binding domain and the C terminal zinc fingers. Overall design: Single cell RNA sequencing was performed to examine the cellular heterogeneity of whole kidney marrow WKM cells in wild type and two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain.,,pubmed:36496511,,IT325 P2 2,GSM6043271,,source name:whole kidney marrow WKM|tissue:whole kidney marrow WKM|age:3 month|genotype/variation:IT325 Mutant WKM cells,IT325 P2 2,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57 207 isoforms derived from 57 207 gene loci with 57 114 isoforms mapping to fully annotated chromosomes 1 to 19  X  Y  M. All isoforms of the same gene were merged to a single gene locus. Furthermore  gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34 111 gene groups. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Assembly: ENCODE VM9 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,whole kidney marrow WKM,No Treatment was performed.,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,Zebrafish strains were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics.,tissue:whole kidney marrow WKM|age:3 month|genotype/variation:IT325 Mutant WKM cells,GSM6043271,GSM6043271: IT325 P2 2; Danio rerio; RNA Seq,GSM6043271 r1,GSM6043271,1,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP370089,,,IT325_P2_2_R1.fastq.gz IT325_P2_2_R2.fastq.gz,fastq fastq,2004851200.0,20048512.0,GSM6043271 r1,0:30 1:70,A:487685629;C:352169841;G:359788661;T:801053801;N:4153268,30,70,,,487685629,352169841,359788661,801053801,4153268,SRX14845526,SRS12600428,SRA1403848,"Sagar, Department of Internal Medicine II, University Medical Center Freiburg","Sagar, Department of Internal Medicine II, University Medical Center Freiburg",2,0.48763,0.86533,0.45772,0.25756,0.99275,0.82568,0.82121,0.68485,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2022-04-13,Adult,Adult,Kidney,Renal System
69499,SRR18745505,SRX14845525,SRS12600427,SRP370089,PRJNA826497,Stage  and cell type specific requirements of ikzf1 during haematopoietic differentiation in zebrafish,GSE200756,Transcriptome Analysis,The zinc finger transcription factor Ikaros1 Ikzf1 is required for lymphoid development in mammals. It is characterized by the presence of four zinc fingers in its DNA binding domain and two zinc fingers in the C terminal protein interaction module. Here  we describe the phenotypes of zebrafish homozygous for two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain. Our results indicate that an intact ikzf1 gene is required for larval T cell development  whereas low levels of adult lymphoid development recover in the mutants. By contrast  the mutants exhibit a signature of increased myelopoiesis at larval and adult stages. Of note  both mutants stimulate erythroid differentiation in larvae  indicating that the C terminal zinc fingers negatively regulate the extent of red blood cell production. An unexpected differential effect of the two mutants on adult erythropoiesis suggests a direct requirement of an intact DNA binding domain for entry of progenitors into the red blood cell lineage. Collectively  our results reinforce the biological differences between larval and adult haematopoiesis  indicate a stage specific function of ikzf1 in regulating the hierarchical bifurcations of differentiation  and assign distinct functions to the DNA binding domain and the C terminal zinc fingers. Overall design: Single cell RNA sequencing was performed to examine the cellular heterogeneity of whole kidney marrow WKM cells in wild type and two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain.,,pubmed:36496511,,IT325 P2 1,GSM6043270,,source name:whole kidney marrow WKM|tissue:whole kidney marrow WKM|age:3 month|genotype/variation:IT325 Mutant WKM cells,IT325 P2 1,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57 207 isoforms derived from 57 207 gene loci with 57 114 isoforms mapping to fully annotated chromosomes 1 to 19  X  Y  M. All isoforms of the same gene were merged to a single gene locus. Furthermore  gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34 111 gene groups. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Assembly: ENCODE VM9 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,whole kidney marrow WKM,No Treatment was performed.,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,Zebrafish strains were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics.,tissue:whole kidney marrow WKM|age:3 month|genotype/variation:IT325 Mutant WKM cells,GSM6043270,GSM6043270: IT325 P2 1; Danio rerio; RNA Seq,GSM6043270 r1,GSM6043270,1,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP370089,,,IT325_P2_1_R1.fastq.gz IT325_P2_1_R2.fastq.gz,fastq fastq,2126689200.0,21266892.0,GSM6043270 r1,0:30 1:70,A:516252796;C:374159868;G:388671448;T:843235579;N:4369509,30,70,,,516252796,374159868,388671448,843235579,4369509,SRX14845525,SRS12600427,SRA1403848,"Sagar, Department of Internal Medicine II, University Medical Center Freiburg","Sagar, Department of Internal Medicine II, University Medical Center Freiburg",2,0.64115,0.86798,0.58644,0.22539,0.99188,0.82065,0.79141,0.64477,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2022-04-13,Adult,Adult,Kidney,Renal System
69500,SRR18745506,SRX14845524,SRS12600426,SRP370089,PRJNA826497,Stage  and cell type specific requirements of ikzf1 during haematopoietic differentiation in zebrafish,GSE200756,Transcriptome Analysis,The zinc finger transcription factor Ikaros1 Ikzf1 is required for lymphoid development in mammals. It is characterized by the presence of four zinc fingers in its DNA binding domain and two zinc fingers in the C terminal protein interaction module. Here  we describe the phenotypes of zebrafish homozygous for two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain. Our results indicate that an intact ikzf1 gene is required for larval T cell development  whereas low levels of adult lymphoid development recover in the mutants. By contrast  the mutants exhibit a signature of increased myelopoiesis at larval and adult stages. Of note  both mutants stimulate erythroid differentiation in larvae  indicating that the C terminal zinc fingers negatively regulate the extent of red blood cell production. An unexpected differential effect of the two mutants on adult erythropoiesis suggests a direct requirement of an intact DNA binding domain for entry of progenitors into the red blood cell lineage. Collectively  our results reinforce the biological differences between larval and adult haematopoiesis  indicate a stage specific function of ikzf1 in regulating the hierarchical bifurcations of differentiation  and assign distinct functions to the DNA binding domain and the C terminal zinc fingers. Overall design: Single cell RNA sequencing was performed to examine the cellular heterogeneity of whole kidney marrow WKM cells in wild type and two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain.,,pubmed:36496511,,IT325 P1 9,GSM6043269,,source name:whole kidney marrow WKM|tissue:whole kidney marrow WKM|age:3 month|genotype/variation:IT325 Mutant WKM cells,IT325 P1 9,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57 207 isoforms derived from 57 207 gene loci with 57 114 isoforms mapping to fully annotated chromosomes 1 to 19  X  Y  M. All isoforms of the same gene were merged to a single gene locus. Furthermore  gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34 111 gene groups. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Assembly: ENCODE VM9 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,whole kidney marrow WKM,No Treatment was performed.,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,Zebrafish strains were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics.,tissue:whole kidney marrow WKM|age:3 month|genotype/variation:IT325 Mutant WKM cells,GSM6043269,GSM6043269: IT325 P1 9; Danio rerio; RNA Seq,GSM6043269 r1,GSM6043269,1,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP370089,,,IT325_P1_9_R1.fastq.gz IT325_P1_9_R2.fastq.gz,fastq fastq,1664318700.0,16643187.0,GSM6043269 r1,0:30 1:70,A:418184224;C:285635872;G:293965577;T:661924855;N:4608172,30,70,,,418184224,285635872,293965577,661924855,4608172,SRX14845524,SRS12600426,SRA1403848,"Sagar, Department of Internal Medicine II, University Medical Center Freiburg","Sagar, Department of Internal Medicine II, University Medical Center Freiburg",2,0.50005,0.83608,0.48126,0.27102,0.99078,0.8184,0.76166,0.64322,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2022-04-13,Adult,Adult,Kidney,Renal System
69501,SRR18745507,SRX14845523,SRS12600425,SRP370089,PRJNA826497,Stage  and cell type specific requirements of ikzf1 during haematopoietic differentiation in zebrafish,GSE200756,Transcriptome Analysis,The zinc finger transcription factor Ikaros1 Ikzf1 is required for lymphoid development in mammals. It is characterized by the presence of four zinc fingers in its DNA binding domain and two zinc fingers in the C terminal protein interaction module. Here  we describe the phenotypes of zebrafish homozygous for two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain. Our results indicate that an intact ikzf1 gene is required for larval T cell development  whereas low levels of adult lymphoid development recover in the mutants. By contrast  the mutants exhibit a signature of increased myelopoiesis at larval and adult stages. Of note  both mutants stimulate erythroid differentiation in larvae  indicating that the C terminal zinc fingers negatively regulate the extent of red blood cell production. An unexpected differential effect of the two mutants on adult erythropoiesis suggests a direct requirement of an intact DNA binding domain for entry of progenitors into the red blood cell lineage. Collectively  our results reinforce the biological differences between larval and adult haematopoiesis  indicate a stage specific function of ikzf1 in regulating the hierarchical bifurcations of differentiation  and assign distinct functions to the DNA binding domain and the C terminal zinc fingers. Overall design: Single cell RNA sequencing was performed to examine the cellular heterogeneity of whole kidney marrow WKM cells in wild type and two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain.,,pubmed:36496511,,IT325 P1 12,GSM6043268,,source name:whole kidney marrow WKM|tissue:whole kidney marrow WKM|age:3 month|genotype/variation:IT325 Mutant WKM cells,IT325 P1 12,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57 207 isoforms derived from 57 207 gene loci with 57 114 isoforms mapping to fully annotated chromosomes 1 to 19  X  Y  M. All isoforms of the same gene were merged to a single gene locus. Furthermore  gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34 111 gene groups. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Assembly: ENCODE VM9 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,whole kidney marrow WKM,No Treatment was performed.,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,Zebrafish strains were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics.,tissue:whole kidney marrow WKM|age:3 month|genotype/variation:IT325 Mutant WKM cells,GSM6043268,GSM6043268: IT325 P1 12; Danio rerio; RNA Seq,GSM6043268 r1,GSM6043268,1,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP370089,,,IT325_P1_12_R1.fastq.gz IT325_P1_12_R2.fastq.gz,fastq fastq,1661691600.0,16616916.0,GSM6043268 r1,0:30 1:70,A:403956788;C:287957287;G:300359489;T:664773989;N:4644047,30,70,,,403956788,287957287,300359489,664773989,4644047,SRX14845523,SRS12600425,SRA1403848,"Sagar, Department of Internal Medicine II, University Medical Center Freiburg","Sagar, Department of Internal Medicine II, University Medical Center Freiburg",2,0.46516,0.85619,0.44488,0.26683,0.9908,0.8296,0.706,0.6762,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2022-04-13,Adult,Adult,Kidney,Renal System
69502,SRR18745508,SRX14845522,SRS12600424,SRP370089,PRJNA826497,Stage  and cell type specific requirements of ikzf1 during haematopoietic differentiation in zebrafish,GSE200756,Transcriptome Analysis,The zinc finger transcription factor Ikaros1 Ikzf1 is required for lymphoid development in mammals. It is characterized by the presence of four zinc fingers in its DNA binding domain and two zinc fingers in the C terminal protein interaction module. Here  we describe the phenotypes of zebrafish homozygous for two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain. Our results indicate that an intact ikzf1 gene is required for larval T cell development  whereas low levels of adult lymphoid development recover in the mutants. By contrast  the mutants exhibit a signature of increased myelopoiesis at larval and adult stages. Of note  both mutants stimulate erythroid differentiation in larvae  indicating that the C terminal zinc fingers negatively regulate the extent of red blood cell production. An unexpected differential effect of the two mutants on adult erythropoiesis suggests a direct requirement of an intact DNA binding domain for entry of progenitors into the red blood cell lineage. Collectively  our results reinforce the biological differences between larval and adult haematopoiesis  indicate a stage specific function of ikzf1 in regulating the hierarchical bifurcations of differentiation  and assign distinct functions to the DNA binding domain and the C terminal zinc fingers. Overall design: Single cell RNA sequencing was performed to examine the cellular heterogeneity of whole kidney marrow WKM cells in wild type and two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain.,,pubmed:36496511,,IT325 P1 11,GSM6043267,,source name:whole kidney marrow WKM|tissue:whole kidney marrow WKM|age:3 month|genotype/variation:IT325 Mutant WKM cells,IT325 P1 11,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57 207 isoforms derived from 57 207 gene loci with 57 114 isoforms mapping to fully annotated chromosomes 1 to 19  X  Y  M. All isoforms of the same gene were merged to a single gene locus. Furthermore  gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34 111 gene groups. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Assembly: ENCODE VM9 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,whole kidney marrow WKM,No Treatment was performed.,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,Zebrafish strains were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics.,tissue:whole kidney marrow WKM|age:3 month|genotype/variation:IT325 Mutant WKM cells,GSM6043267,GSM6043267: IT325 P1 11; Danio rerio; RNA Seq,GSM6043267 r1,GSM6043267,1,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP370089,,,IT325_P1_11_R1.fastq.gz IT325_P1_11_R2.fastq.gz,fastq fastq,1649804700.0,16498047.0,GSM6043267 r1,0:30 1:70,A:421610227;C:284430368;G:293792368;T:645440352;N:4531385,30,70,,,421610227,284430368,293792368,645440352,4531385,SRX14845522,SRS12600424,SRA1403848,"Sagar, Department of Internal Medicine II, University Medical Center Freiburg","Sagar, Department of Internal Medicine II, University Medical Center Freiburg",2,0.49467,0.83409,0.47999,0.32463,0.99072,0.8258,0.74421,0.68286,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2022-04-13,Adult,Adult,Kidney,Renal System
69503,SRR18745509,SRX14845521,SRS12600423,SRP370089,PRJNA826497,Stage  and cell type specific requirements of ikzf1 during haematopoietic differentiation in zebrafish,GSE200756,Transcriptome Analysis,The zinc finger transcription factor Ikaros1 Ikzf1 is required for lymphoid development in mammals. It is characterized by the presence of four zinc fingers in its DNA binding domain and two zinc fingers in the C terminal protein interaction module. Here  we describe the phenotypes of zebrafish homozygous for two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain. Our results indicate that an intact ikzf1 gene is required for larval T cell development  whereas low levels of adult lymphoid development recover in the mutants. By contrast  the mutants exhibit a signature of increased myelopoiesis at larval and adult stages. Of note  both mutants stimulate erythroid differentiation in larvae  indicating that the C terminal zinc fingers negatively regulate the extent of red blood cell production. An unexpected differential effect of the two mutants on adult erythropoiesis suggests a direct requirement of an intact DNA binding domain for entry of progenitors into the red blood cell lineage. Collectively  our results reinforce the biological differences between larval and adult haematopoiesis  indicate a stage specific function of ikzf1 in regulating the hierarchical bifurcations of differentiation  and assign distinct functions to the DNA binding domain and the C terminal zinc fingers. Overall design: Single cell RNA sequencing was performed to examine the cellular heterogeneity of whole kidney marrow WKM cells in wild type and two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain.,,pubmed:36496511,,IT325 P1 10,GSM6043266,,source name:whole kidney marrow WKM|tissue:whole kidney marrow WKM|age:3 month|genotype/variation:IT325 Mutant WKM cells,IT325 P1 10,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57 207 isoforms derived from 57 207 gene loci with 57 114 isoforms mapping to fully annotated chromosomes 1 to 19  X  Y  M. All isoforms of the same gene were merged to a single gene locus. Furthermore  gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34 111 gene groups. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Assembly: ENCODE VM9 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,whole kidney marrow WKM,No Treatment was performed.,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,Zebrafish strains were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics.,tissue:whole kidney marrow WKM|age:3 month|genotype/variation:IT325 Mutant WKM cells,GSM6043266,GSM6043266: IT325 P1 10; Danio rerio; RNA Seq,GSM6043266 r1,GSM6043266,1,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP370089,,,IT325_P1_10_R1.fastq.gz IT325_P1_10_R2.fastq.gz,fastq fastq,1586719700.0,15867197.0,GSM6043266 r1,0:30 1:70,A:401941369;C:273093096;G:285633018;T:621609734;N:4442483,30,70,,,401941369,273093096,285633018,621609734,4442483,SRX14845521,SRS12600423,SRA1403848,"Sagar, Department of Internal Medicine II, University Medical Center Freiburg","Sagar, Department of Internal Medicine II, University Medical Center Freiburg",2,0.4951,0.81744,0.4671,0.28736,0.99247,0.8337,0.59663,0.70252,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2022-04-13,Adult,Adult,Kidney,Renal System
69504,SRR18745513,SRX14845520,SRS12600422,SRP370089,PRJNA826497,Stage  and cell type specific requirements of ikzf1 during haematopoietic differentiation in zebrafish,GSE200756,Transcriptome Analysis,The zinc finger transcription factor Ikaros1 Ikzf1 is required for lymphoid development in mammals. It is characterized by the presence of four zinc fingers in its DNA binding domain and two zinc fingers in the C terminal protein interaction module. Here  we describe the phenotypes of zebrafish homozygous for two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain. Our results indicate that an intact ikzf1 gene is required for larval T cell development  whereas low levels of adult lymphoid development recover in the mutants. By contrast  the mutants exhibit a signature of increased myelopoiesis at larval and adult stages. Of note  both mutants stimulate erythroid differentiation in larvae  indicating that the C terminal zinc fingers negatively regulate the extent of red blood cell production. An unexpected differential effect of the two mutants on adult erythropoiesis suggests a direct requirement of an intact DNA binding domain for entry of progenitors into the red blood cell lineage. Collectively  our results reinforce the biological differences between larval and adult haematopoiesis  indicate a stage specific function of ikzf1 in regulating the hierarchical bifurcations of differentiation  and assign distinct functions to the DNA binding domain and the C terminal zinc fingers. Overall design: Single cell RNA sequencing was performed to examine the cellular heterogeneity of whole kidney marrow WKM cells in wild type and two distinct mutant ikzf1 alleles. The IT325 variant lacks the C terminal two zinc fingers  whereas the fr105 variant retains only the first zinc finger of the DNA binding domain.,,pubmed:36496511,,FR105 P2 8,GSM6043265,,source name:whole kidney marrow WKM|tissue:whole kidney marrow WKM|age:3 month|genotype/variation:FR105 Mutant WKM cells,FR105 P2 8,For image aquisition  intensity extraction and basecalling HiSeq Control Software  2.0.2  RTA 2.4.11 / Recipe Fragment 2.0.0.2​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14 Paired end reads were aligned to the transcriptome using bwa version 0.6.2 r126 with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57 207 isoforms derived from 57 207 gene loci with 57 114 isoforms mapping to fully annotated chromosomes 1 to 19  X  Y  M. All isoforms of the same gene were merged to a single gene locus. Furthermore  gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34 111 gene groups. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier UMI. The remainder of the left read contains a polyT stretch. The left read was not used for quantification. For each cell barcode  the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus. Based on binomial statistics  the number of observed UMIs was converted into transcript counts Gruen et al.  2014. Assembly: ENCODE VM9 Supplementary files format and content: CSV files  columns represent each cell barcode total barcodes used = 192  rows represent the geneid and the values in the file are the quantified number of transcripts.,whole kidney marrow WKM,No Treatment was performed.,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,Zebrafish strains were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics.,tissue:whole kidney marrow WKM|age:3 month|genotype/variation:FR105 Mutant WKM cells,GSM6043265,GSM6043265: FR105 P2 8; Danio rerio; RNA Seq,GSM6043265 r1,GSM6043265,1,Three mpf wild type and mutant adult zebrafish were anaesthetized with 0.02% tricaine before kidney collection. A ventral  midline incision was made and kidney were dissected and placed into ice cold 0.9× PBS containing 5% FCS. Single cell suspensions were generated by aspiration followed by gentle 'teasing' of each organ on a 40 μm nylon mesh filter with a plunger from a 1 ml syringe. As described in CEL Seq2 protocol Hashimshony et al. 2016 Adapted from TruSeq Small RNA Library Preparation Protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP370089,,,FR105_P2_8_R1.fastq.gz FR105_P2_8_R2.fastq.gz,fastq fastq,1820400900.0,18204009.0,GSM6043265 r1,0:30 1:70,A:455432253;C:315216381;G:325597472;T:720478774;N:3676020,30,70,,,455432253,315216381,325597472,720478774,3676020,SRX14845520,SRS12600422,SRA1403848,"Sagar, Department of Internal Medicine II, University Medical Center Freiburg","Sagar, Department of Internal Medicine II, University Medical Center Freiburg",2,0.41746,0.83035,0.38398,0.31189,0.99235,0.83844,0.93052,0.66092,30,70,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,Germany,2022-04-13,Adult,Adult,Kidney,Renal System