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130 rows where experiment.library_layout = "PAIRED", technology = "celseq" and tissue_curation_coarse = "Cardiovascular System"

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devstage_curation_coarse 4

devstage_curation 4

tissue_curation 2

experiment.library_source 2

tissue_curation_coarse 1

  • Cardiovascular System · 130 ✖

technology 1

  • celseq · 130 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_selection 1

experiment.library_layout 1

  • PAIRED · 130 ✖
Link 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
43755 43755 SRR6054093 SRX3201032 SRS2528004 SRP118319 PRJNA408129 Spatially resolved RNA sequencing of the embryonic zebrafish heart GSE104057 Transcriptome Analysis Development of specialized cell types and structures in the vertebrate heart is regulated by spatially restricted molecular pathways. Disruptions in these pathways can cause severe congenital cardiac malformations or functional defects. To better understand these pathways and how they regulate cardiac development and function we used tomo seq combining high throughput RNA sequencing with tissue sectioning to establish a genome wide expression dataset with high spatial resolution for the developing zebrafish heart. Analysis of the dataset revealed over 1100 genes differentially expressed in sub compartments. Pacemaker cells in the sinoatrial region induce heart contractions but little is known about the mechanisms underlying their development and function. Using our transcriptome map we identified spatially restricted Wnt/ß catenin signaling activity in pacemaker cells which was controlled by Islet 1 activity. Moreover Wnt/ß catenin signaling at a specific developmental stage in the myocardium controls heart rate by regulating pacemaker cellular response to parasympathetic stimuli. Thus this high resolution transcriptome map incorporating all cell types in the embryonic heart can expose spatially restricted molecular pathways critical for specific cardiac functions. Overall design: To generate spatially resolved RNA seq data for the developing zebrafish hearts 2 dpf we cryosectioned 3 hearts extracted RNA from the individual sections 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. Sample Heart #1 is the primary sample. Heart #2 and #3 are biological replicates used for comparison.   pubmed:29400650   heart3 2dpf wt GSM2788520   source name:isolated embryonic heart|tissue:embryonic heart|developmental stage:48 hpf direction:posterior/inflow tract to anterior/outflow tract; located in sections #11 #39|section thickness:10µm sections heart3 2dpf wt 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 processed data files contain transcript read counts normalized against spike in read count and total read count per section Genome build: zv9 with improved three prime annotation see Junker et al 2014 Cell Supplementary files format and content: csv file containing transcript counts per gene rows and section columns isolated embryonic heart Unfixed embryonic hearts were dissected 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:embryonic heart|developmental stage:48 hpf direction:posterior/inflow tract to anterior/outflow tract; located in sections #11 #39|section thickness:10µm sections GSM2788520 GSM2788520: heart3 2dpf wt; Danio rerio; RNA Seq GSM2788520   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 GEO Accession:GSM2788520 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP118319     heart_03_SB032dpfwt_R1.fastq.gz heart_03_SB032dpfwt_R2.fastq.gz fastq fastq 2662906147.0 17670214.0 GSM2788520 r1 0:75.39 1:75.31 A:828280216;C:376671462;G:437493213;T:1019745554;N:715702 75 75     828280216 376671462 437493213 1019745554 715702 SRX3201032 SRS2528004 SRA610777 GEO Jeroen Bakkers lab, Cardiac Development and Genetics, Hubrecht Institute 2 0.04145 0.36579 0.03839 0.09603 0.99912 0.89623 0.41379 0.5674 76 75 T B mate1 technical by mapping diff illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2017-09-20 Hatching Embryo Heart Cardiovascular System
43756 43756 SRR6054092 SRX3201031 SRS2528003 SRP118319 PRJNA408129 Spatially resolved RNA sequencing of the embryonic zebrafish heart GSE104057 Transcriptome Analysis Development of specialized cell types and structures in the vertebrate heart is regulated by spatially restricted molecular pathways. Disruptions in these pathways can cause severe congenital cardiac malformations or functional defects. To better understand these pathways and how they regulate cardiac development and function we used tomo seq combining high throughput RNA sequencing with tissue sectioning to establish a genome wide expression dataset with high spatial resolution for the developing zebrafish heart. Analysis of the dataset revealed over 1100 genes differentially expressed in sub compartments. Pacemaker cells in the sinoatrial region induce heart contractions but little is known about the mechanisms underlying their development and function. Using our transcriptome map we identified spatially restricted Wnt/ß catenin signaling activity in pacemaker cells which was controlled by Islet 1 activity. Moreover Wnt/ß catenin signaling at a specific developmental stage in the myocardium controls heart rate by regulating pacemaker cellular response to parasympathetic stimuli. Thus this high resolution transcriptome map incorporating all cell types in the embryonic heart can expose spatially restricted molecular pathways critical for specific cardiac functions. Overall design: To generate spatially resolved RNA seq data for the developing zebrafish hearts 2 dpf we cryosectioned 3 hearts extracted RNA from the individual sections 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. Sample Heart #1 is the primary sample. Heart #2 and #3 are biological replicates used for comparison.   pubmed:29400650   heart2 2dpf wt GSM2788519   source name:isolated embryonic heart|tissue:embryonic heart|developmental stage:48 hpf direction:posterior/inflow tract to anterior/outflow tract; located in sections #49 #96|section thickness:10µm sections heart2 2dpf wt 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 processed data files contain transcript read counts normalized against spike in read count and total read count per section Genome build: zv9 with improved three prime annotation see Junker et al 2014 Cell Supplementary files format and content: csv file containing transcript counts per gene rows and section columns isolated embryonic heart Unfixed embryonic hearts were dissected 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:embryonic heart|developmental stage:48 hpf direction:posterior/inflow tract to anterior/outflow tract; located in sections #49 #96|section thickness:10µm sections GSM2788519 GSM2788519: heart2 2dpf wt; Danio rerio; RNA Seq GSM2788519   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 GEO Accession:GSM2788519 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP118319     heart_02_SB-150707_R1.fastq.gz heart_02_SB-150707_R2.fastq.gz fastq fastq 5482437730.0 36337096.0 GSM2788519 r1 0:75.41 1:75.47 A:1859596349;C:686627791;G:950285046;T:1980208127;N:5720417 75 75     1859596349 686627791 950285046 1980208127 5720417 SRX3201031 SRS2528003 SRA610777 GEO Jeroen Bakkers lab, Cardiac Development and Genetics, Hubrecht Institute 2 0.14301 0.55835 0.12504 0.16935 0.99285 0.86334 0.46837 0.58661 76 74 T B mate1 technical by mapping diff illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2017-09-20 Hatching Embryo Heart Cardiovascular System
43757 43757 SRR6054091 SRX3201030 SRS2528002 SRP118319 PRJNA408129 Spatially resolved RNA sequencing of the embryonic zebrafish heart GSE104057 Transcriptome Analysis Development of specialized cell types and structures in the vertebrate heart is regulated by spatially restricted molecular pathways. Disruptions in these pathways can cause severe congenital cardiac malformations or functional defects. To better understand these pathways and how they regulate cardiac development and function we used tomo seq combining high throughput RNA sequencing with tissue sectioning to establish a genome wide expression dataset with high spatial resolution for the developing zebrafish heart. Analysis of the dataset revealed over 1100 genes differentially expressed in sub compartments. Pacemaker cells in the sinoatrial region induce heart contractions but little is known about the mechanisms underlying their development and function. Using our transcriptome map we identified spatially restricted Wnt/ß catenin signaling activity in pacemaker cells which was controlled by Islet 1 activity. Moreover Wnt/ß catenin signaling at a specific developmental stage in the myocardium controls heart rate by regulating pacemaker cellular response to parasympathetic stimuli. Thus this high resolution transcriptome map incorporating all cell types in the embryonic heart can expose spatially restricted molecular pathways critical for specific cardiac functions. Overall design: To generate spatially resolved RNA seq data for the developing zebrafish hearts 2 dpf we cryosectioned 3 hearts extracted RNA from the individual sections 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. Sample Heart #1 is the primary sample. Heart #2 and #3 are biological replicates used for comparison.   pubmed:29400650   heart1 2dpf wt GSM2788518   source name:isolated embryonic heart|tissue:embryonic heart|developmental stage:48 hpf direction:anterior/outflow tract to posterior/inflow tract; located in sections #2 #41|section thickness:10µm sections heart1 2dpf wt 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 processed data files contain transcript read counts normalized against spike in read count and total read count per section Genome build: zv9 with improved three prime annotation see Junker et al 2014 Cell Supplementary files format and content: csv file containing transcript counts per gene rows and section columns isolated embryonic heart Unfixed embryonic hearts were dissected 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:embryonic heart|developmental stage:48 hpf direction:anterior/outflow tract to posterior/inflow tract; located in sections #2 #41|section thickness:10µm sections GSM2788518 GSM2788518: heart1 2dpf wt; Danio rerio; RNA Seq GSM2788518   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 GEO Accession:GSM2788518 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP118319     heart_01_SB-06-2dpf_wt_R2.fastq.gz heart_01_SB-06-2dpf_wt_R1.fastq.gz fastq fastq 8152229052.0 54104958.0 GSM2788518 r1 0:75.41 1:75.27 A:2955268830;C:1118145970;G:1152323290;T:2924136690;N:2354272 75 75     2955268830 1118145970 1152323290 2924136690 2354272 SRX3201030 SRS2528002 SRA610777 GEO Jeroen Bakkers lab, Cardiac Development and Genetics, Hubrecht Institute 2 0.02706 0.26955 0.01984 0.05871 0.99675 0.93194 0.37979 0.63172 76 76 T B mate1 technical by mapping diff illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2017-09-20 Hatching Embryo Heart Cardiovascular System
47897 47897 SRR6908713 SRX3856801 SRS3100393 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM6 lymphocytes GSM3070139   tissue:WKM6 lymphocytes|FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM6 lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM6 lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070139 GSM3070139: WKM6 lymphocytes; Danio rerio; RNA Seq GSM3070139   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070139 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM6_lymphocytes_L001_R1_001.fastq.gz WKM6_lymphocytes_L001_R2_001.fastq.gz fastq fastq 1092718271.0 7238113.0 GSM3070139 r1 0:75.49 1:75.48 A:308417237;C:162459915;G:183666585;T:438104581;N:69953 75 75     308417237 162459915 183666585 438104581 69953 SRX3856801 SRS3100393 SRA675960 GEO Hubrecht Institute 2 0.33032 0.81969 0.25647 0.49446 0.98587 0.93105 0.47765 0.53939 75 76 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Lymphatic System Cardiovascular System
47898 47898 SRR6908714 SRX3856801 SRS3100393 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM6 lymphocytes GSM3070139   tissue:WKM6 lymphocytes|FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM6 lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM6 lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070139 GSM3070139: WKM6 lymphocytes; Danio rerio; RNA Seq GSM3070139   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070139 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM6_lymphocytes_L002_R1_001.fastq.gz WKM6_lymphocytes_L002_R2_001.fastq.gz fastq fastq 988686695.0 6550079.0 GSM3070139 r2 0:75.49 1:75.46 A:281384679;C:146335731;G:165878017;T:395040397;N:47871 75 75     281384679 146335731 165878017 395040397 47871 SRX3856801 SRS3100393 SRA675960 GEO Hubrecht Institute 2 0.31311 0.79325 0.23663 0.48843 0.99034 0.95471 0.47178 0.54622 75 76 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Lymphatic System Cardiovascular System
47899 47899 SRR6908715 SRX3856801 SRS3100393 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM6 lymphocytes GSM3070139   tissue:WKM6 lymphocytes|FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM6 lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM6 lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070139 GSM3070139: WKM6 lymphocytes; Danio rerio; RNA Seq GSM3070139   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070139 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM6_lymphocytes_L003_R1_001.fastq.gz WKM6_lymphocytes_L003_R2_001.fastq.gz fastq fastq 965970467.0 6397966.0 GSM3070139 r3 0:75.51 1:75.47 A:271037832;C:143188198;G:162584210;T:389145889;N:14338 75 75     271037832 143188198 162584210 389145889 14338 SRX3856801 SRS3100393 SRA675960 GEO Hubrecht Institute 2 0.2983 0.81397 0.23255 0.49479 0.99377 0.94379 0.43187 0.54702 76 76 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Lymphatic System Cardiovascular System
47900 47900 SRR6908716 SRX3856801 SRS3100393 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM6 lymphocytes GSM3070139   tissue:WKM6 lymphocytes|FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM6 lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM6 lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM6|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070139 GSM3070139: WKM6 lymphocytes; Danio rerio; RNA Seq GSM3070139   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070139 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM6_lymphocytes_L004_R1_001.fastq.gz WKM6_lymphocytes_L004_R2_001.fastq.gz fastq fastq 845107841.0 5598430.0 GSM3070139 r4 0:75.50 1:75.46 A:239787549;C:124312776;G:144002735;T:336997076;N:7705 75 75     239787549 124312776 144002735 336997076 7705 SRX3856801 SRS3100393 SRA675960 GEO Hubrecht Institute 2 0.27606 0.8077 0.21352 0.49895 0.99502 0.95511 0.37654 0.5537 76 76 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Lymphatic System Cardiovascular System
47905 47905 SRR6908705 SRX3856799 SRS3100391 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM5 lymphocytes GSM3070137   tissue:WKM5 lymphocytes|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM5 lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM5 lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070137 GSM3070137: WKM5 lymphocytes; Danio rerio; RNA Seq GSM3070137   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070137 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM5_lymphocytes_L001_R1_001.fastq.gz WKM5_lymphocytes_L001_R2_001.fastq.gz fastq fastq 989705998.0 6559370.0 GSM3070137 r1 0:75.45 1:75.43 A:297302138;C:149495824;G:174348330;T:368343979;N:215727 75 75     297302138 149495824 174348330 368343979 215727 SRX3856799 SRS3100391 SRA675960 GEO Hubrecht Institute 2 0.24742 0.6658 0.20828 0.41062 0.98214 0.85423 0.46204 0.47999 76 76 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Lymphatic System Cardiovascular System
47906 47906 SRR6908706 SRX3856799 SRS3100391 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM5 lymphocytes GSM3070137   tissue:WKM5 lymphocytes|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM5 lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM5 lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070137 GSM3070137: WKM5 lymphocytes; Danio rerio; RNA Seq GSM3070137   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070137 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM5_lymphocytes_L002_R1_001.fastq.gz WKM5_lymphocytes_L002_R2_001.fastq.gz fastq fastq 966752947.0 6406981.0 GSM3070137 r2 0:75.44 1:75.45 A:289601664;C:144620642;G:173993992;T:358339663;N:196986 75 75     289601664 144620642 173993992 358339663 196986 SRX3856799 SRS3100391 SRA675960 GEO Hubrecht Institute 2 0.23604 0.65405 0.20033 0.39718 0.98196 0.8636 0.50139 0.50729 74 76 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Lymphatic System Cardiovascular System
47907 47907 SRR6908707 SRX3856799 SRS3100391 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM5 lymphocytes GSM3070137   tissue:WKM5 lymphocytes|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM5 lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM5 lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070137 GSM3070137: WKM5 lymphocytes; Danio rerio; RNA Seq GSM3070137   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070137 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM5_lymphocytes_L003_R1_001.fastq.gz WKM5_lymphocytes_L003_R2_001.fastq.gz fastq fastq 958861430.0 6354224.0 GSM3070137 r3 0:75.46 1:75.44 A:286188763;C:145686623;G:169054587;T:357878024;N:53433 75 75     286188763 145686623 169054587 357878024 53433 SRX3856799 SRS3100391 SRA675960 GEO Hubrecht Institute 2 0.25215 0.67286 0.20951 0.41571 0.98707 0.84611 0.45707 0.51523 75 75 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Lymphatic System Cardiovascular System
47908 47908 SRR6908708 SRX3856799 SRS3100391 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM5 lymphocytes GSM3070137   tissue:WKM5 lymphocytes|FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM5 lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM5 lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM5|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070137 GSM3070137: WKM5 lymphocytes; Danio rerio; RNA Seq GSM3070137   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070137 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM5_lymphocytes_L004_R2_001.fastq.gz WKM5_lymphocytes_L004_R1_001.fastq.gz fastq fastq 907053718.0 6010618.0 GSM3070137 r4 0:75.45 1:75.46 A:270238988;C:137187310;G:162483694;T:337104230;N:39496 75 75     270238988 137187310 162483694 337104230 39496 SRX3856799 SRS3100391 SRA675960 GEO Hubrecht Institute 2 0.2382 0.66089 0.20055 0.40225 0.98537 0.86109 0.4862 0.51182 75 74 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Lymphatic System Cardiovascular System
47953 47953 SRR6908655 SRX3856786 SRS3100377 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM10 lymphocytes GSM3070125   tissue:WKM10 lymphocytes|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM10 lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM10 lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070125 GSM3070125: WKM10 lymphocytes; Danio rerio; RNA Seq GSM3070125   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070125 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM10_lymphocytes_L001_R1_001.fastq.gz WKM10_lymphocytes_L001_R2_001.fastq.gz fastq fastq 1505229869.0 9975689.0 GSM3070125 r1 0:75.46 1:75.43 A:446863117;C:223332557;G:257023910;T:577686078;N:324207 75 75     446863117 223332557 257023910 577686078 324207 SRX3856786 SRS3100377 SRA675960 GEO Hubrecht Institute 2 0.27651 0.70172 0.22976 0.41642 0.98198 0.85401 0.46672 0.52056 75 76 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Lymphatic System Cardiovascular System
47954 47954 SRR6908656 SRX3856786 SRS3100377 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM10 lymphocytes GSM3070125   tissue:WKM10 lymphocytes|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM10 lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM10 lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070125 GSM3070125: WKM10 lymphocytes; Danio rerio; RNA Seq GSM3070125   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070125 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM10_lymphocytes_L002_R1_001.fastq.gz WKM10_lymphocytes_L002_R2_001.fastq.gz fastq fastq 1466970503.0 9721974.0 GSM3070125 r2 0:75.45 1:75.44 A:434939637;C:215624726;G:255310153;T:560791208;N:304779 75 75     434939637 215624726 255310153 560791208 304779 SRX3856786 SRS3100377 SRA675960 GEO Hubrecht Institute 2 0.263 0.6934 0.21939 0.4057 0.98127 0.86417 0.4805 0.49132 75 76 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Lymphatic System Cardiovascular System
47955 47955 SRR6908657 SRX3856786 SRS3100377 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM10 lymphocytes GSM3070125   tissue:WKM10 lymphocytes|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM10 lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM10 lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070125 GSM3070125: WKM10 lymphocytes; Danio rerio; RNA Seq GSM3070125   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070125 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM10_lymphocytes_L003_R2_001.fastq.gz WKM10_lymphocytes_L003_R1_001.fastq.gz fastq fastq 1456610152.0 9652493.0 GSM3070125 r3 0:75.46 1:75.44 A:429303329;C:217559734;G:249207876;T:560459433;N:79780 75 75     429303329 217559734 249207876 560459433 79780 SRX3856786 SRS3100377 SRA675960 GEO Hubrecht Institute 2 0.28238 0.70747 0.2323 0.4212 0.98683 0.84575 0.43386 0.5155 76 75 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Lymphatic System Cardiovascular System
47956 47956 SRR6908658 SRX3856786 SRS3100377 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM10 lymphocytes GSM3070125   tissue:WKM10 lymphocytes|FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM10 lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM10 lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM10|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070125 GSM3070125: WKM10 lymphocytes; Danio rerio; RNA Seq GSM3070125   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070125 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM10_lymphocytes_L004_R1_001.fastq.gz WKM10_lymphocytes_L004_R2_001.fastq.gz fastq fastq 1372270103.0 9093444.0 GSM3070125 r4 0:75.46 1:75.45 A:404750065;C:203942354;G:237441524;T:526077075;N:59085 75 75     404750065 203942354 237441524 526077075 59085 SRX3856786 SRS3100377 SRA675960 GEO Hubrecht Institute 2 0.2714 0.69516 0.22843 0.40836 0.98602 0.8607 0.47846 0.52284 76 76 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Lymphatic System Cardiovascular System
55365 55365 SRR10321288 SRX7032108 SRS5552214 SRP226527 PRJNA578764 Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart. GSE139218 Transcriptome Analysis While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.   pubmed:31868166   FK2 GSM4134187   source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle FK2 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: text files: read count matrices in which rows correspond to genes and columns to single cells. Tgnppa:mCitrine ventricle 7dpi Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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|tissue:Adult zebrafish ventricle GSM4134187 GSM4134187: FK2; Danio rerio; RNA Seq GSM4134187   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:GSM4134187 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP226527     Fk-2_H3MHFBGXY_S4_L001_R1_001.fastq.gz Fk-2_H3MHFBGXY_S4_L001_R2_001.fastq.gz fastq fastq 2747645940.0 18195462.0 GSM4134187 r1 0:75.51 1:75.50 A:761850296;C:390951746;G:422952266;T:1169751842;N:2139790 75 75     761850296 390951746 422952266 1169751842 2139790 SRX7032108 SRS5552214 SRA982819 GEO Bakkers, Hubrecht Institute 2 0.23534 0.89135 0.19366 0.15359 0.99902 0.86636 0.40119 0.71094 75 76 T B mate1 technical by mapping diff illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2019-10-21 Multi-stage Multi-stage Heart Cardiovascular System
55366 55366 SRR10321289 SRX7032108 SRS5552214 SRP226527 PRJNA578764 Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart. GSE139218 Transcriptome Analysis While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.   pubmed:31868166   FK2 GSM4134187   source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle FK2 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: text files: read count matrices in which rows correspond to genes and columns to single cells. Tgnppa:mCitrine ventricle 7dpi Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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|tissue:Adult zebrafish ventricle GSM4134187 GSM4134187: FK2; Danio rerio; RNA Seq GSM4134187   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:GSM4134187 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP226527     Fk-2_H3MHFBGXY_S4_L002_R1_001.fastq.gz Fk-2_H3MHFBGXY_S4_L002_R2_001.fastq.gz fastq fastq 2719577388.0 18010558.0 GSM4134187 r2 0:75.50 1:75.50 A:750500832;C:383761329;G:435629268;T:1147504474;N:2181485 75 75     750500832 383761329 435629268 1147504474 2181485 SRX7032108 SRS5552214 SRA982819 GEO Bakkers, Hubrecht Institute 2 0.21913 0.88799 0.16554 0.15559 0.99855 0.8704 0.48175 0.71083 76 76 T B mate1 technical by mapping diff illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2019-10-21 Multi-stage Multi-stage Heart Cardiovascular System
55367 55367 SRR10321290 SRX7032108 SRS5552214 SRP226527 PRJNA578764 Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart. GSE139218 Transcriptome Analysis While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.   pubmed:31868166   FK2 GSM4134187   source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle FK2 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: text files: read count matrices in which rows correspond to genes and columns to single cells. Tgnppa:mCitrine ventricle 7dpi Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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|tissue:Adult zebrafish ventricle GSM4134187 GSM4134187: FK2; Danio rerio; RNA Seq GSM4134187   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:GSM4134187 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP226527     Fk-2_H3MHFBGXY_S4_L003_R1_001.fastq.gz Fk-2_H3MHFBGXY_S4_L003_R2_001.fastq.gz fastq fastq 2396848795.0 15867573.0 GSM4134187 r3 0:75.56 1:75.50 A:649358056;C:340829352;G:366620430;T:1039511314;N:529643 75 75     649358056 340829352 366620430 1039511314 529643 SRX7032108 SRS5552214 SRA982819 GEO Bakkers, Hubrecht Institute 2 0.22581 0.89171 0.18682 0.15894 0.99928 0.87054 0.41592 0.70495 75 76 T B mate1 technical by mapping diff illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2019-10-21 Multi-stage Multi-stage Heart Cardiovascular System
55368 55368 SRR10321291 SRX7032108 SRS5552214 SRP226527 PRJNA578764 Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart. GSE139218 Transcriptome Analysis While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.   pubmed:31868166   FK2 GSM4134187   source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle FK2 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: text files: read count matrices in which rows correspond to genes and columns to single cells. Tgnppa:mCitrine ventricle 7dpi Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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|tissue:Adult zebrafish ventricle GSM4134187 GSM4134187: FK2; Danio rerio; RNA Seq GSM4134187   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:GSM4134187 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP226527     Fk-2_H3MHFBGXY_S4_L004_R1_001.fastq.gz Fk-2_H3MHFBGXY_S4_L004_R2_001.fastq.gz fastq fastq 2610671390.0 17282452.0 GSM4134187 r4 0:75.56 1:75.50 A:691899084;C:368646569;G:415634004;T:1133907995;N:583738 75 75     691899084 368646569 415634004 1133907995 583738 SRX7032108 SRS5552214 SRA982819 GEO Bakkers, Hubrecht Institute 2 0.24107 0.8886 0.19934 0.15491 0.99926 0.8702 0.31578 0.66998 76 76 T B mate1 technical by mapping diff illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2019-10-21 Multi-stage Multi-stage Heart Cardiovascular System
55369 55369 SRR10321284 SRX7032107 SRS5552213 SRP226527 PRJNA578764 Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart. GSE139218 Transcriptome Analysis While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.   pubmed:31868166   FK1 GSM4134186   source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle FK1 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: text files: read count matrices in which rows correspond to genes and columns to single cells. Tgnppa:mCitrine ventricle 7dpi Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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|tissue:Adult zebrafish ventricle GSM4134186 GSM4134186: FK1; Danio rerio; RNA Seq GSM4134186   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:GSM4134186 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP226527     FK-1_H3MHFBGXY_S3_L001_R1_001.fastq.gz FK-1_H3MHFBGXY_S3_L001_R2_001.fastq.gz fastq fastq 2366670719.0 15672127.0 GSM4134186 r1 0:75.50 1:75.51 A:648000254;C:343663478;G:358343004;T:1014831853;N:1832130 75 75     648000254 343663478 358343004 1014831853 1832130 SRX7032107 SRS5552213 SRA982819 GEO Bakkers, Hubrecht Institute 2 0.30353 0.90485 0.25842 0.14878 0.99912 0.85857 0.23863 0.71645 76 75 T B mate1 technical by mapping diff illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2019-10-21 Multi-stage Multi-stage Heart Cardiovascular System
55370 55370 SRR10321285 SRX7032107 SRS5552213 SRP226527 PRJNA578764 Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart. GSE139218 Transcriptome Analysis While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.   pubmed:31868166   FK1 GSM4134186   source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle FK1 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: text files: read count matrices in which rows correspond to genes and columns to single cells. Tgnppa:mCitrine ventricle 7dpi Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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|tissue:Adult zebrafish ventricle GSM4134186 GSM4134186: FK1; Danio rerio; RNA Seq GSM4134186   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:GSM4134186 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP226527     FK-1_H3MHFBGXY_S3_L002_R1_001.fastq.gz FK-1_H3MHFBGXY_S3_L002_R2_001.fastq.gz fastq fastq 2360571906.0 15632617.0 GSM4134186 r2 0:75.49 1:75.51 A:643644738;C:339965378;G:371359828;T:1003716606;N:1885356 75 75     643644738 339965378 371359828 1003716606 1885356 SRX7032107 SRS5552213 SRA982819 GEO Bakkers, Hubrecht Institute                       T B mate1 technical by mapping diff illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2019-10-21 Multi-stage Multi-stage Heart Cardiovascular System
55371 55371 SRR10321286 SRX7032107 SRS5552213 SRP226527 PRJNA578764 Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart. GSE139218 Transcriptome Analysis While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.   pubmed:31868166   FK1 GSM4134186   source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle FK1 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: text files: read count matrices in which rows correspond to genes and columns to single cells. Tgnppa:mCitrine ventricle 7dpi Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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|tissue:Adult zebrafish ventricle GSM4134186 GSM4134186: FK1; Danio rerio; RNA Seq GSM4134186   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:GSM4134186 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP226527     FK-1_H3MHFBGXY_S3_L003_R1_001.fastq.gz FK-1_H3MHFBGXY_S3_L003_R2_001.fastq.gz fastq fastq 2074411223.0 13732357.0 GSM4134186 r3 0:75.55 1:75.51 A:554276583;C:300804770;G:312025485;T:906833457;N:470928 75 75     554276583 300804770 312025485 906833457 470928 SRX7032107 SRS5552213 SRA982819 GEO Bakkers, Hubrecht Institute 2 0.2996 0.90397 0.25521 0.15245 0.99933 0.86314 0.21969 0.69653 75 76 T B mate1 technical by mapping diff illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2019-10-21 Multi-stage Multi-stage Heart Cardiovascular System
55372 55372 SRR10321287 SRX7032107 SRS5552213 SRP226527 PRJNA578764 Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart. GSE139218 Transcriptome Analysis While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.   pubmed:31868166   FK1 GSM4134186   source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle FK1 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: text files: read count matrices in which rows correspond to genes and columns to single cells. Tgnppa:mCitrine ventricle 7dpi Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP 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|tissue:Adult zebrafish ventricle GSM4134186 GSM4134186: FK1; Danio rerio; RNA Seq GSM4134186   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:GSM4134186 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP226527     FK-1_H3MHFBGXY_S3_L004_R1_001.fastq.gz FK-1_H3MHFBGXY_S3_L004_R2_001.fastq.gz fastq fastq 2267459781.0 15009993.0 GSM4134186 r4 0:75.55 1:75.51 A:592957170;C:326713096;G:354670327;T:992614149;N:505039 75 75     592957170 326713096 354670327 992614149 505039 SRX7032107 SRS5552213 SRA982819 GEO Bakkers, Hubrecht Institute 2 0.3137 0.9006 0.26295 0.14953 0.99914 0.8622 0.19895 0.70141 76 76 T B mate1 technical by mapping diff illumina nextseq unknown poly_a trueseq sc single_cell_plate celseq   Netherlands 2019-10-21 Multi-stage Multi-stage Heart Cardiovascular System
59985 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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. Fro…       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 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. Fro…       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 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. Fro…       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 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. Fro…       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 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. Fro…       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 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. Fro…       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 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. Fro…       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 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. Fro…       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 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. Fro…       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 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. Fro…       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 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. Fro…       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 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. Fro…       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 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. Fro…       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 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. Fro…       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 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. Fro…       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 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. Fro…       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 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. Fro…       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 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. Fro…       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 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. Fro…       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 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. Fro…       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 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. Fro…       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 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. Fro…       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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;