metadata: run_metadata: 73 rows where experiment.library_selection = "cDNA", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and technology = "celseq"

73 rows where experiment.library_selection = "cDNA", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and technology = "celseq"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	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.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	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.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	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
71397	71397	SRR21571181	SRX17573445	SRS15113179	SRP397130	PRJNA880596	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]	GSE213359	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed	parent bioproject:PRJNA880593		TIE:EGFP MCR:MCS Tumor 2 GFP+ #3	GSM6580971	source name:MCR:MCS Melanoma\|tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+\|geo loc name:missing\|collection date:missing	TIE:EGFP MCR:MCS Tumor 2 GFP+ #3	The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv	MCR:MCS Melanoma	Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	N/A	tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+	GSM6580971	GSM6580971: TIE:EGFP MCR:MCS Tumor 2 GFP+ #3; Danio rerio; RNA Seq	GSM6580971 r1	GSM6580971	1	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP397130		HAR-HN-s014.R1.fastq.gz HAR-HN-s014.R2.fastq.gz	fastq fastq	2393526200.0	27831700.0	GSM6580971 r1	0:26 1:60	A:587629810;C:436040251;G:440163052;T:929430783;N:262304	26	60	587629810	436040251	440163052	929430783	262304	SRX17573445	SRS15113179			Oncology/Hematology, Boston Children's Hospital	2	0.1102	0.89036	0.10359	0.25006	0.99285	0.81172	0.56209	0.58312	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	United States	2022-09-14	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
71398	71398	SRR21571182	SRX17573444	SRS15113178	SRP397130	PRJNA880596	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]	GSE213359	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed	parent bioproject:PRJNA880593		TIE:EGFP MCR:MCS Tumor 2 GFP /mCherry+	GSM6580970	source name:MCR:MCS Melanoma\|tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP /mCherry+\|geo loc name:missing\|collection date:missing	TIE:EGFP MCR:MCS Tumor 2 GFP /mCherry+	The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv	MCR:MCS Melanoma	Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	N/A	tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP /mCherry+	GSM6580970	GSM6580970: TIE:EGFP MCR:MCS Tumor 2 GFP /mCherry+; Danio rerio; RNA Seq	GSM6580970 r1	GSM6580970	1	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP397130		HAR-HN-s013.R1.fastq.gz HAR-HN-s013.R2.fastq.gz	fastq fastq	2799404318.0	32551213.0	GSM6580970 r1	0:26 1:60	A:674562015;C:518279489;G:507732521;T:1093251404;N:5578889	26	60	674562015	518279489	507732521	1093251404	5578889	SRX17573444	SRS15113178			Oncology/Hematology, Boston Children's Hospital	2	0.11385	0.89818	0.10608	0.24805	0.99162	0.80519	0.57833	0.58452	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	United States	2022-09-14	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
71399	71399	SRR21571183	SRX17573443	SRS15113177	SRP397130	PRJNA880596	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]	GSE213359	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed	parent bioproject:PRJNA880593		TIE:EGFP MCR:MCS Tumor 2 GFP+ #2	GSM6580969	source name:MCR:MCS Melanoma\|tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+\|geo loc name:missing\|collection date:missing	TIE:EGFP MCR:MCS Tumor 2 GFP+ #2	The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv	MCR:MCS Melanoma	Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	N/A	tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+	GSM6580969	GSM6580969: TIE:EGFP MCR:MCS Tumor 2 GFP+ #2; Danio rerio; RNA Seq	GSM6580969 r1	GSM6580969	1	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP397130		HAR-HN-s012.R1.fastq.gz HAR-HN-s012.R2.fastq.gz	fastq fastq	2643515042.0	30738547.0	GSM6580969 r1	0:26 1:60	A:644064543;C:487933120;G:466421088;T:1039827853;N:5268438	26	60	644064543	487933120	466421088	1039827853	5268438	SRX17573443	SRS15113177			Oncology/Hematology, Boston Children's Hospital	2	0.11114	0.8924	0.10417	0.25808	0.99151	0.80499	0.60121	0.567	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	United States	2022-09-14	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
71400	71400	SRR21571184	SRX17573442	SRS15113176	SRP397130	PRJNA880596	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]	GSE213359	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed	parent bioproject:PRJNA880593		TIE:EGFP MCR:MCS Tumor 2 GFP+ #1	GSM6580968	source name:MCR:MCS Melanoma\|tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+\|geo loc name:missing\|collection date:missing	TIE:EGFP MCR:MCS Tumor 2 GFP+ #1	The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv	MCR:MCS Melanoma	Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	N/A	tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+	GSM6580968	GSM6580968: TIE:EGFP MCR:MCS Tumor 2 GFP+ #1; Danio rerio; RNA Seq	GSM6580968 r1	GSM6580968	1	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP397130		HAR-HN-s011.R1.fastq.gz HAR-HN-s011.R2.fastq.gz	fastq fastq	2701784858.0	31416103.0	GSM6580968 r1	0:26 1:60	A:654129800;C:498352764;G:495215316;T:1048678271;N:5408707	26	60	654129800	498352764	495215316	1048678271	5408707	SRX17573442	SRS15113176			Oncology/Hematology, Boston Children's Hospital	2	0.10435	0.89555	0.0971	0.26327	0.99354	0.80647	0.56789	0.50648	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	United States	2022-09-14	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
71401	71401	SRR21571185	SRX17573441	SRS15113175	SRP397130	PRJNA880596	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]	GSE213359	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed	parent bioproject:PRJNA880593		TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #3	GSM6580967	source name:MCR:SATB2 Melanoma\|tissue:MCR:SATB2 Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+\|geo loc name:missing\|collection date:missing	TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #3	The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv	MCR:SATB2 Melanoma	Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	N/A	tissue:MCR:SATB2 Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+	GSM6580967	GSM6580967: TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #3; Danio rerio; RNA Seq	GSM6580967 r1	GSM6580967	1	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP397130		HAR-HN-s007.R1.fastq.gz HAR-HN-s007.R2.fastq.gz	fastq fastq	3169503770.0	36854695.0	GSM6580967 r1	0:26 1:60	A:758395203;C:580012810;G:565741250;T:1265023729;N:330778	26	60	758395203	580012810	565741250	1265023729	330778	SRX17573441	SRS15113175			Oncology/Hematology, Boston Children's Hospital	2	0.11903	0.89395	0.11159	0.29218	0.99243	0.79705	0.54327	0.56983	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	United States	2022-09-14	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
71402	71402	SRR21571186	SRX17573440	SRS15113174	SRP397130	PRJNA880596	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]	GSE213359	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed	parent bioproject:PRJNA880593		TIE:EGFP MCR:SATB2 Tumor 1 GFP /mCherry+	GSM6580966	source name:MCR:SATB2 Melanoma\|tissue:MCR:SATB2 Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP /mCherry+\|geo loc name:missing\|collection date:missing	TIE:EGFP MCR:SATB2 Tumor 1 GFP /mCherry+	The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv	MCR:SATB2 Melanoma	Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	N/A	tissue:MCR:SATB2 Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP /mCherry+	GSM6580966	GSM6580966: TIE:EGFP MCR:SATB2 Tumor 1 GFP /mCherry+; Danio rerio; RNA Seq	GSM6580966 r1	GSM6580966	1	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP397130		HAR-HN-s006.R1.fastq.gz HAR-HN-s006.R2.fastq.gz	fastq fastq	3401223030.0	39549105.0	GSM6580966 r1	0:26 1:60	A:811721089;C:634467013;G:610447766;T:1344233621;N:353541	26	60	811721089	634467013	610447766	1344233621	353541	SRX17573440	SRS15113174			Oncology/Hematology, Boston Children's Hospital	2	0.11728	0.9042	0.11084	0.22711	0.9931	0.79494	0.65306	0.56756	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	United States	2022-09-14	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
71403	71403	SRR21571187	SRX17573439	SRS15113173	SRP397130	PRJNA880596	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]	GSE213359	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed	parent bioproject:PRJNA880593		TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #2	GSM6580965	source name:MCR:SATB2 Melanoma\|tissue:MCR:SATB2 Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+\|geo loc name:missing\|collection date:missing	TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #2	The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv	MCR:SATB2 Melanoma	Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	N/A	tissue:MCR:SATB2 Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+	GSM6580965	GSM6580965: TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #2; Danio rerio; RNA Seq	GSM6580965 r1	GSM6580965	1	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP397130		HAR-HN-s005.R1.fastq.gz HAR-HN-s005.R2.fastq.gz	fastq fastq	3042431718.0	35377113.0	GSM6580965 r1	0:26 1:60	A:744782141;C:565144430;G:541953297;T:1190237432;N:314418	26	60	744782141	565144430	541953297	1190237432	314418	SRX17573439	SRS15113173			Oncology/Hematology, Boston Children's Hospital	2	0.11149	0.88671	0.10471	0.23988	0.99162	0.79543	0.64395	0.58192	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	United States	2022-09-14	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
71404	71404	SRR21571188	SRX17573438	SRS15113172	SRP397130	PRJNA880596	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]	GSE213359	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed	parent bioproject:PRJNA880593		TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #1	GSM6580964	source name:MCR:SATB2 Melanoma\|tissue:MCR:SATB2 Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+\|geo loc name:missing\|collection date:missing	TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #1	The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv	MCR:SATB2 Melanoma	Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	N/A	tissue:MCR:SATB2 Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+	GSM6580964	GSM6580964: TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #1; Danio rerio; RNA Seq	GSM6580964 r1	GSM6580964	1	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP397130		HAR-HN-s004.R1.fastq.gz HAR-HN-s004.R2.fastq.gz	fastq fastq	3454727328.0	40171248.0	GSM6580964 r1	0:26 1:60	A:823342460;C:630914117;G:615200919;T:1384911330;N:358502	26	60	823342460	630914117	615200919	1384911330	358502	SRX17573438	SRS15113172			Oncology/Hematology, Boston Children's Hospital	2	0.12493	0.8892	0.11706	0.21947	0.99314	0.79216	0.73215	0.53614	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	United States	2022-09-14	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
71405	71405	SRR21571189	SRX17573437	SRS15113171	SRP397130	PRJNA880596	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]	GSE213359	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed	parent bioproject:PRJNA880593		TIE:EGFP MCR:MCS Tumor 1 GFP+ #3	GSM6580963	source name:MCR:MCS Melanoma\|tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+\|geo loc name:missing\|collection date:missing	TIE:EGFP MCR:MCS Tumor 1 GFP+ #3	The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv	MCR:MCS Melanoma	Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	N/A	tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+	GSM6580963	GSM6580963: TIE:EGFP MCR:MCS Tumor 1 GFP+ #3; Danio rerio; RNA Seq	GSM6580963 r1	GSM6580963	1	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP397130		HAR-SW-s016.R1.fastq.gz HAR-SW-s016.R2.fastq.gz	fastq fastq	2986527160.0	34727060.0	GSM6580963 r1	0:26 1:60	A:741435297;C:548375629;G:534147329;T:1162130158;N:438747	26	60	741435297	548375629	534147329	1162130158	438747	SRX17573437	SRS15113171			Oncology/Hematology, Boston Children's Hospital	2	0.12032	0.87963	0.11182	0.30887	0.99145	0.79926	0.53199	0.59453	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	United States	2022-09-14	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
71406	71406	SRR21571190	SRX17573436	SRS15113170	SRP397130	PRJNA880596	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]	GSE213359	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed	parent bioproject:PRJNA880593		TIE:EGFP MCR:MCS Tumor 1 mCherry+;GFP	GSM6580962	source name:MCR:MCS Melanoma\|tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:mCherry+;GFP \|geo loc name:missing\|collection date:missing	TIE:EGFP MCR:MCS Tumor 1 mCherry+;GFP	The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv	MCR:MCS Melanoma	Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	N/A	tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:mCherry+;GFP	GSM6580962	GSM6580962: TIE:EGFP MCR:MCS Tumor 1 mCherry+;GFP ; Danio rerio; RNA Seq	GSM6580962 r1	GSM6580962	1	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP397130		HAR-SW-s015.R1.fastq.gz HAR-SW-s015.R2.fastq.gz	fastq fastq	2668318990.0	31026965.0	GSM6580962 r1	0:26 1:60	A:650521761;C:486885070;G:465311971;T:1065210518;N:389670	26	60	650521761	486885070	465311971	1065210518	389670	SRX17573436	SRS15113170			Oncology/Hematology, Boston Children's Hospital	2	0.1142	0.88526	0.10718	0.34648	0.99198	0.80428	0.56024	0.56437	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	United States	2022-09-14	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
71407	71407	SRR21571191	SRX17573435	SRS15113168	SRP397130	PRJNA880596	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]	GSE213359	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed	parent bioproject:PRJNA880593		TIE:EGFP MCR:MCS Tumor 1 GFP+ #2	GSM6580961	source name:MCR:MCS Melanoma\|tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+\|geo loc name:missing\|collection date:missing	TIE:EGFP MCR:MCS Tumor 1 GFP+ #2	The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv	MCR:MCS Melanoma	Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	N/A	tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+	GSM6580961	GSM6580961: TIE:EGFP MCR:MCS Tumor 1 GFP+ #2; Danio rerio; RNA Seq	GSM6580961 r1	GSM6580961	1	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP397130		HAR-SW-s014.R1.fastq.gz HAR-SW-s014.R2.fastq.gz	fastq fastq	2393946138.0	27836583.0	GSM6580961 r1	0:26 1:60	A:596410784;C:437801560;G:418907527;T:940499589;N:326678	26	60	596410784	437801560	418907527	940499589	326678	SRX17573435	SRS15113168			Oncology/Hematology, Boston Children's Hospital	2	0.12342	0.85959	0.11689	0.34528	0.98965	0.80472	0.49199	0.56661	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	United States	2022-09-14	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
71408	71408	SRR21571192	SRX17573434	SRS15113169	SRP397130	PRJNA880596	A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT seq]	GSE213359	Transcriptome Analysis	Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: SORT seq TIE:EGFP+ melanomas scRNA seq of zebrafish melanomas expressing TIE:EGFP 2 MCR:MCS tumors expressing TIE:EGFP were processed 1 MCR:SATB2 tumor expressing TIE:EGFP was processed	parent bioproject:PRJNA880593		TIE:EGFP MCR:MCS Tumor 1 GFP+ #1	GSM6580960	source name:MCR:MCS Melanoma\|tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+\|geo loc name:missing\|collection date:missing	TIE:EGFP MCR:MCS Tumor 1 GFP+ #1	The single cell sort seq data are analyzed using the scruff R package Single Cell RNA Seq UMI Filtering Facilitator following the pipeline in https://github.com/campbio/scruff. The raw fastq files are first demultiplexed and aligned to zebrafish reference genome GRCz11 using Rsubread and UMI filtered count matrix are generated. Assembly: GRCz11 Supplementary files format and content: Count matrix table tsv	MCR:MCS Melanoma	Zebrafish melanomas overexpressing empty multiple cloning site MCS or SATB2 vectors.	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	N/A	tissue:MCR:MCS Melanoma\|genotype:expressing TIE:EGFP\|sorted cells:GFP+	GSM6580960	GSM6580960: TIE:EGFP MCR:MCS Tumor 1 GFP+ #1; Danio rerio; RNA Seq	GSM6580960 r1	GSM6580960	1	Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase Sigma #5401119001 in DMEM Gibco #11965 092 with 1% Penstrep Corning #30 002 CI. Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer PBS/ 10%FBS/1% Penstrep before filtering through a FACs tube Corning #352235. Single cells were sorted into 384 well cell capture plates containing barcoded primers from Single Cell Discoveries https://www.scdiscoveries.com/ using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP ;mCherry+ cells. Library preparation and Illumina sequencing was performed by Single Cell Discoveries. SORT seq	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP397130		HAR-SW-s013.R1.fastq.gz HAR-SW-s013.R2.fastq.gz	fastq fastq	3043161084.0	35385594.0	GSM6580960 r1	0:26 1:60	A:750431276;C:555809857;G:537628053;T:1198847837;N:444061	26	60	750431276	555809857	537628053	1198847837	444061	SRX17573434	SRS15113169			Oncology/Hematology, Boston Children's Hospital	2	0.11034	0.86528	0.10371	0.32665	0.99198	0.79695	0.51927	0.58318	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq	United States	2022-09-14	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
73951	73951	SRR23290994	SRX19234275	SRS16638733	SRP420309	PRJNA929990	Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration	GSE224156	Other	Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.		pubmed:37200435	zfCM 21dpi 2	GSM7016815	source name:Heart\|tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:21dpi\|geo loc name:missing\|collection date:missing	zfCM 21dpi 2	Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.	Heart	Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.		tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:21dpi	GSM7016815	GSM7016815: zfCM 21dpi 2; Danio rerio; RNA Seq	GSM7016815 r1	GSM7016815	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP420309		HUB-PN-s041_H7L35BGXM_S4_L001_R1_001.fastq.gz HUB-PN-s041_H7L35BGXM_S4_L001_R2_001.fastq.gz	fastq fastq	858173876.0	9978766.0	GSM7016815 r1	0:26 1:60	A:213059809;C:160771814;G:156105199;T:328218073;N:18981	26	60	213059809	160771814	156105199	328218073	18981	SRX19234275	SRS16638733	SRA1583767	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	2	0.11426	0.88222	0.10668	0.29657	0.99149	0.8355	0.60863	0.67263	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2023-01-31	Undetermined	Undetermined	Heart	Cardiovascular System
73952	73952	SRR23290995	SRX19234275	SRS16638733	SRP420309	PRJNA929990	Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration	GSE224156	Other	Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.		pubmed:37200435	zfCM 21dpi 2	GSM7016815	source name:Heart\|tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:21dpi\|geo loc name:missing\|collection date:missing	zfCM 21dpi 2	Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.	Heart	Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.		tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:21dpi	GSM7016815	GSM7016815: zfCM 21dpi 2; Danio rerio; RNA Seq	GSM7016815 r1	GSM7016815	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP420309		HUB-PN-s041_H7L35BGXM_S4_L002_R1_001.fastq.gz HUB-PN-s041_H7L35BGXM_S4_L002_R2_001.fastq.gz	fastq fastq	843721318.0	9810713.0	GSM7016815 r2	0:26 1:60	A:208714473;C:157371099;G:155893107;T:321724427;N:18212	26	60	208714473	157371099	155893107	321724427	18212	SRX19234275	SRS16638733	SRA1583767	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	2	0.11232	0.8799	0.10497	0.29809	0.99123	0.83621	0.66836	0.66521	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2023-01-31	Undetermined	Undetermined	Heart	Cardiovascular System
73953	73953	SRR23290996	SRX19234275	SRS16638733	SRP420309	PRJNA929990	Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration	GSE224156	Other	Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.		pubmed:37200435	zfCM 21dpi 2	GSM7016815	source name:Heart\|tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:21dpi\|geo loc name:missing\|collection date:missing	zfCM 21dpi 2	Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.	Heart	Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.		tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:21dpi	GSM7016815	GSM7016815: zfCM 21dpi 2; Danio rerio; RNA Seq	GSM7016815 r1	GSM7016815	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP420309		HUB-PN-s041_H7L35BGXM_S4_L003_R1_001.fastq.gz HUB-PN-s041_H7L35BGXM_S4_L003_R2_001.fastq.gz	fastq fastq	864128860.0	10048010.0	GSM7016815 r3	0:26 1:60	A:214256028;C:161957471;G:157308166;T:330585259;N:21936	26	60	214256028	161957471	157308166	330585259	21936	SRX19234275	SRS16638733	SRA1583767	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	2	0.1147	0.88514	0.10704	0.29827	0.99105	0.83321	0.67314	0.65637	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2023-01-31	Undetermined	Undetermined	Heart	Cardiovascular System
73954	73954	SRR23290997	SRX19234275	SRS16638733	SRP420309	PRJNA929990	Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration	GSE224156	Other	Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.		pubmed:37200435	zfCM 21dpi 2	GSM7016815	source name:Heart\|tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:21dpi\|geo loc name:missing\|collection date:missing	zfCM 21dpi 2	Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.	Heart	Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.		tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:21dpi	GSM7016815	GSM7016815: zfCM 21dpi 2; Danio rerio; RNA Seq	GSM7016815 r1	GSM7016815	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP420309		HUB-PN-s041_H7L35BGXM_S4_L004_R1_001.fastq.gz HUB-PN-s041_H7L35BGXM_S4_L004_R2_001.fastq.gz	fastq fastq	862094960.0	10024360.0	GSM7016815 r4	0:26 1:60	A:212975380;C:160923939;G:159237695;T:328939876;N:18070	26	60	212975380	160923939	159237695	328939876	18070	SRX19234275	SRS16638733	SRA1583767	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	2	0.11191	0.88105	0.10467	0.2945	0.99151	0.83623	0.67428	0.67156	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2023-01-31	Undetermined	Undetermined	Heart	Cardiovascular System
73955	73955	SRR23290998	SRX19234274	SRS16638732	SRP420309	PRJNA929990	Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration	GSE224156	Other	Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.		pubmed:37200435	zfCM 7dpi 4	GSM7016814	source name:Heart\|tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi\|geo loc name:missing\|collection date:missing	zfCM 7dpi 4	Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.	Heart	Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.		tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi	GSM7016814	GSM7016814: zfCM 7dpi 4; Danio rerio; RNA Seq	GSM7016814 r1	GSM7016814	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP420309		HUB-PN-s039_H7L35BGXM_S3_L001_R1_001.fastq.gz HUB-PN-s039_H7L35BGXM_S3_L001_R2_001.fastq.gz	fastq fastq	839750096.0	9764536.0	GSM7016814 r1	0:26 1:60	A:207245393;C:152642612;G:152075698;T:327767742;N:18651	26	60	207245393	152642612	152075698	327767742	18651	SRX19234274	SRS16638732	SRA1583767	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	2	0.10807	0.88063	0.1011	0.31218	0.99133	0.81844	0.57963	0.58371	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2023-01-31	Undetermined	Undetermined	Heart	Cardiovascular System
73956	73956	SRR23290999	SRX19234274	SRS16638732	SRP420309	PRJNA929990	Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration	GSE224156	Other	Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.		pubmed:37200435	zfCM 7dpi 4	GSM7016814	source name:Heart\|tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi\|geo loc name:missing\|collection date:missing	zfCM 7dpi 4	Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.	Heart	Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.		tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi	GSM7016814	GSM7016814: zfCM 7dpi 4; Danio rerio; RNA Seq	GSM7016814 r1	GSM7016814	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP420309		HUB-PN-s039_H7L35BGXM_S3_L002_R1_001.fastq.gz HUB-PN-s039_H7L35BGXM_S3_L002_R2_001.fastq.gz	fastq fastq	824555530.0	9587855.0	GSM7016814 r2	0:26 1:60	A:202762477;C:149247401;G:151695233;T:320832302;N:18117	26	60	202762477	149247401	151695233	320832302	18117	SRX19234274	SRS16638732	SRA1583767	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	2	0.10764	0.87478	0.1005	0.31049	0.99101	0.81929	0.58127	0.51321	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2023-01-31	Undetermined	Undetermined	Heart	Cardiovascular System
73957	73957	SRR23291000	SRX19234274	SRS16638732	SRP420309	PRJNA929990	Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration	GSE224156	Other	Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.		pubmed:37200435	zfCM 7dpi 4	GSM7016814	source name:Heart\|tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi\|geo loc name:missing\|collection date:missing	zfCM 7dpi 4	Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.	Heart	Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.		tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi	GSM7016814	GSM7016814: zfCM 7dpi 4; Danio rerio; RNA Seq	GSM7016814 r1	GSM7016814	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP420309		HUB-PN-s039_H7L35BGXM_S3_L003_R1_001.fastq.gz HUB-PN-s039_H7L35BGXM_S3_L003_R2_001.fastq.gz	fastq fastq	845111766.0	9826881.0	GSM7016814 r3	0:26 1:60	A:208286833;C:153694024;G:153159692;T:329951816;N:19401	26	60	208286833	153694024	153159692	329951816	19401	SRX19234274	SRS16638732	SRA1583767	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	2	0.1087	0.88111	0.10148	0.31291	0.99068	0.81698	0.55014	0.58727	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2023-01-31	Undetermined	Undetermined	Heart	Cardiovascular System
73958	73958	SRR23291001	SRX19234274	SRS16638732	SRP420309	PRJNA929990	Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration	GSE224156	Other	Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.		pubmed:37200435	zfCM 7dpi 4	GSM7016814	source name:Heart\|tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi\|geo loc name:missing\|collection date:missing	zfCM 7dpi 4	Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.	Heart	Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.		tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi	GSM7016814	GSM7016814: zfCM 7dpi 4; Danio rerio; RNA Seq	GSM7016814 r1	GSM7016814	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP420309		HUB-PN-s039_H7L35BGXM_S3_L004_R1_001.fastq.gz HUB-PN-s039_H7L35BGXM_S3_L004_R2_001.fastq.gz	fastq fastq	842710216.0	9798956.0	GSM7016814 r4	0:26 1:60	A:206896294;C:152644705;G:155014140;T:328138108;N:16969	26	60	206896294	152644705	155014140	328138108	16969	SRX19234274	SRS16638732	SRA1583767	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	2	0.10766	0.87731	0.10058	0.31053	0.99119	0.81781	0.57185	0.57715	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2023-01-31	Undetermined	Undetermined	Heart	Cardiovascular System
73959	73959	SRR23291002	SRX19234273	SRS16638731	SRP420309	PRJNA929990	Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration	GSE224156	Other	Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.		pubmed:37200435	zfCM 21dpi 1	GSM7016813	source name:Heart\|tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:21dpi\|geo loc name:missing\|collection date:missing	zfCM 21dpi 1	Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.	Heart	Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.		tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:21dpi	GSM7016813	GSM7016813: zfCM 21dpi 1; Danio rerio; RNA Seq	GSM7016813 r1	GSM7016813	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP420309		HUB-PN-025_HCMYKBGXC_S8_L001_R1_001.fastq.gz HUB-PN-025_HCMYKBGXC_S8_L001_R2_001.fastq.gz	fastq fastq	638322358.0	7422353.0	GSM7016813 r1	0:26 1:60	A:152993677;C:129279491;G:116490423;T:238075133;N:1483634	26	60	152993677	129279491	116490423	238075133	1483634	SRX19234273	SRS16638731	SRA1583767	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	2	0.1186	0.92133	0.11281	0.53473	0.99391	0.89818	0.6282	0.56941	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2023-01-31	Undetermined	Undetermined	Heart	Cardiovascular System
73960	73960	SRR23291003	SRX19234273	SRS16638731	SRP420309	PRJNA929990	Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration	GSE224156	Other	Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.		pubmed:37200435	zfCM 21dpi 1	GSM7016813	source name:Heart\|tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:21dpi\|geo loc name:missing\|collection date:missing	zfCM 21dpi 1	Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.	Heart	Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.		tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:21dpi	GSM7016813	GSM7016813: zfCM 21dpi 1; Danio rerio; RNA Seq	GSM7016813 r1	GSM7016813	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP420309		HUB-PN-025_HCMYKBGXC_S8_L002_R1_001.fastq.gz HUB-PN-025_HCMYKBGXC_S8_L002_R2_001.fastq.gz	fastq fastq	633345022.0	7364477.0	GSM7016813 r2	0:26 1:60	A:150874121;C:127629476;G:118171343;T:235389766;N:1280316	26	60	150874121	127629476	118171343	235389766	1280316	SRX19234273	SRS16638731	SRA1583767	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	2	0.11665	0.91596	0.11139	0.53318	0.99425	0.89822	0.64949	0.56009	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2023-01-31	Undetermined	Undetermined	Heart	Cardiovascular System
73961	73961	SRR23291004	SRX19234273	SRS16638731	SRP420309	PRJNA929990	Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration	GSE224156	Other	Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.		pubmed:37200435	zfCM 21dpi 1	GSM7016813	source name:Heart\|tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:21dpi\|geo loc name:missing\|collection date:missing	zfCM 21dpi 1	Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.	Heart	Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.		tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:21dpi	GSM7016813	GSM7016813: zfCM 21dpi 1; Danio rerio; RNA Seq	GSM7016813 r1	GSM7016813	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP420309		HUB-PN-025_HCMYKBGXC_S8_L003_R1_001.fastq.gz HUB-PN-025_HCMYKBGXC_S8_L003_R2_001.fastq.gz	fastq fastq	643723416.0	7485156.0	GSM7016813 r3	0:26 1:60	A:154277144;C:130529094;G:117635488;T:240275453;N:1006237	26	60	154277144	130529094	117635488	240275453	1006237	SRX19234273	SRS16638731	SRA1583767	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	2	0.11809	0.9216	0.11258	0.53566	0.99397	0.89871	0.63435	0.55308	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2023-01-31	Undetermined	Undetermined	Heart	Cardiovascular System
73962	73962	SRR23291005	SRX19234273	SRS16638731	SRP420309	PRJNA929990	Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration	GSE224156	Other	Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.		pubmed:37200435	zfCM 21dpi 1	GSM7016813	source name:Heart\|tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:21dpi\|geo loc name:missing\|collection date:missing	zfCM 21dpi 1	Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.	Heart	Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.		tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:21dpi	GSM7016813	GSM7016813: zfCM 21dpi 1; Danio rerio; RNA Seq	GSM7016813 r1	GSM7016813	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP420309		HUB-PN-025_HCMYKBGXC_S8_L004_R1_001.fastq.gz HUB-PN-025_HCMYKBGXC_S8_L004_R2_001.fastq.gz	fastq fastq	632759362.0	7357667.0	GSM7016813 r4	0:26 1:60	A:150797181;C:127674217;G:117974605;T:235361625;N:951734	26	60	150797181	127674217	117974605	235361625	951734	SRX19234273	SRS16638731	SRA1583767	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	2	0.11662	0.91609	0.11147	0.53237	0.99381	0.89775	0.65781	0.55524	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2023-01-31	Undetermined	Undetermined	Heart	Cardiovascular System
73963	73963	SRR23291006	SRX19234272	SRS16638730	SRP420309	PRJNA929990	Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration	GSE224156	Other	Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.		pubmed:37200435	zfCM 7dpi 3	GSM7016812	source name:Heart\|tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi\|geo loc name:missing\|collection date:missing	zfCM 7dpi 3	Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.	Heart	Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.		tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi	GSM7016812	GSM7016812: zfCM 7dpi 3; Danio rerio; RNA Seq	GSM7016812 r1	GSM7016812	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP420309		HUB-DB-006_HNWVVBGX9_S5_L001_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L001_R2_001.fastq.gz	fastq fastq	929999528.0	10813948.0	GSM7016812 r1	0:26 1:60	A:240334465;C:174255952;G:184260587;T:330943403;N:205121	26	60	240334465	174255952	184260587	330943403	205121	SRX19234272	SRS16638730	SRA1583767	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	2	0.11116	0.87404	0.10307	0.43901	0.99178	0.93034	0.6268	0.44639	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2023-01-31	Undetermined	Undetermined	Heart	Cardiovascular System
73964	73964	SRR23291007	SRX19234272	SRS16638730	SRP420309	PRJNA929990	Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration	GSE224156	Other	Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.		pubmed:37200435	zfCM 7dpi 3	GSM7016812	source name:Heart\|tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi\|geo loc name:missing\|collection date:missing	zfCM 7dpi 3	Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.	Heart	Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.		tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi	GSM7016812	GSM7016812: zfCM 7dpi 3; Danio rerio; RNA Seq	GSM7016812 r1	GSM7016812	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP420309		HUB-DB-006_HNWVVBGX9_S5_L002_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L002_R2_001.fastq.gz	fastq fastq	987824896.0	11486336.0	GSM7016812 r2	0:26 1:60	A:251121714;C:184449811;G:201317783;T:350692225;N:243363	26	60	251121714	184449811	201317783	350692225	243363	SRX19234272	SRS16638730	SRA1583767	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	2	0.11269	0.87873	0.10426	0.44461	0.99172	0.92506	0.6241	0.4506	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2023-01-31	Undetermined	Undetermined	Heart	Cardiovascular System
73965	73965	SRR23291008	SRX19234272	SRS16638730	SRP420309	PRJNA929990	Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration	GSE224156	Other	Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.		pubmed:37200435	zfCM 7dpi 3	GSM7016812	source name:Heart\|tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi\|geo loc name:missing\|collection date:missing	zfCM 7dpi 3	Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.	Heart	Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.		tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi	GSM7016812	GSM7016812: zfCM 7dpi 3; Danio rerio; RNA Seq	GSM7016812 r1	GSM7016812	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP420309		HUB-DB-006_HNWVVBGX9_S5_L003_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L003_R2_001.fastq.gz	fastq fastq	959933032.0	11162012.0	GSM7016812 r3	0:26 1:60	A:247983556;C:179564753;G:190342582;T:341858456;N:183685	26	60	247983556	179564753	190342582	341858456	183685	SRX19234272	SRS16638730	SRA1583767	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	2	0.11176	0.87161	0.10342	0.43986	0.99155	0.93026	0.63442	0.44405	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2023-01-31	Undetermined	Undetermined	Heart	Cardiovascular System
73966	73966	SRR23291009	SRX19234272	SRS16638730	SRP420309	PRJNA929990	Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration	GSE224156	Other	Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.		pubmed:37200435	zfCM 7dpi 3	GSM7016812	source name:Heart\|tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi\|geo loc name:missing\|collection date:missing	zfCM 7dpi 3	Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.	Heart	Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.		tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi	GSM7016812	GSM7016812: zfCM 7dpi 3; Danio rerio; RNA Seq	GSM7016812 r1	GSM7016812	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP420309		HUB-DB-006_HNWVVBGX9_S5_L004_R1_001.fastq.gz HUB-DB-006_HNWVVBGX9_S5_L004_R2_001.fastq.gz	fastq fastq	798370766.0	9283381.0	GSM7016812 r4	0:26 1:60	A:205538880;C:148510556;G:161196381;T:282964175;N:160774	26	60	205538880	148510556	161196381	282964175	160774	SRX19234272	SRS16638730	SRA1583767	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	2	0.11014	0.87018	0.10209	0.43668	0.9921	0.93346	0.56645	0.44683	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2023-01-31	Undetermined	Undetermined	Heart	Cardiovascular System
73967	73967	SRR23291010	SRX19234271	SRS16638729	SRP420309	PRJNA929990	Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration	GSE224156	Other	Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.		pubmed:37200435	zfCM 7dpi 2	GSM7016811	source name:Heart\|tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi\|geo loc name:missing\|collection date:missing	zfCM 7dpi 2	Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.	Heart	Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.		tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi	GSM7016811	GSM7016811: zfCM 7dpi 2; Danio rerio; RNA Seq	GSM7016811 r1	GSM7016811	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP420309		HUB-DB-005_HNWVVBGX9_S4_L001_R1_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L001_R2_001.fastq.gz	fastq fastq	806178534.0	9374169.0	GSM7016811 r1	0:26 1:60	A:213590554;C:148614157;G:163804315;T:279996916;N:172592	26	60	213590554	148614157	163804315	279996916	172592	SRX19234271	SRS16638729	SRA1583767	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	2	0.10778	0.79221	0.1011	0.39378	0.99299	0.93695	0.65894	0.39542	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2023-01-31	Undetermined	Undetermined	Heart	Cardiovascular System
73968	73968	SRR23291011	SRX19234271	SRS16638729	SRP420309	PRJNA929990	Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration	GSE224156	Other	Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.		pubmed:37200435	zfCM 7dpi 2	GSM7016811	source name:Heart\|tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi\|geo loc name:missing\|collection date:missing	zfCM 7dpi 2	Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.	Heart	Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.		tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi	GSM7016811	GSM7016811: zfCM 7dpi 2; Danio rerio; RNA Seq	GSM7016811 r1	GSM7016811	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP420309		HUB-DB-005_HNWVVBGX9_S4_L002_R1_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L002_R2_001.fastq.gz	fastq fastq	874594286.0	10169701.0	GSM7016811 r2	0:26 1:60	A:227213153;C:160851586;G:182364146;T:303951184;N:214217	26	60	227213153	160851586	182364146	303951184	214217	SRX19234271	SRS16638729	SRA1583767	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	2	0.11066	0.80318	0.10409	0.40131	0.99289	0.9333	0.66859	0.40896	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2023-01-31	Undetermined	Undetermined	Heart	Cardiovascular System
73969	73969	SRR23291012	SRX19234271	SRS16638729	SRP420309	PRJNA929990	Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration	GSE224156	Other	Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.		pubmed:37200435	zfCM 7dpi 2	GSM7016811	source name:Heart\|tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi\|geo loc name:missing\|collection date:missing	zfCM 7dpi 2	Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.	Heart	Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.		tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi	GSM7016811	GSM7016811: zfCM 7dpi 2; Danio rerio; RNA Seq	GSM7016811 r1	GSM7016811	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP420309		HUB-DB-005_HNWVVBGX9_S4_L003_R1_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L003_R2_001.fastq.gz	fastq fastq	831835860.0	9672510.0	GSM7016811 r3	0:26 1:60	A:220300204;C:153061412;G:168938657;T:289375449;N:160138	26	60	220300204	153061412	168938657	289375449	160138	SRX19234271	SRS16638729	SRA1583767	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	2	0.10977	0.78663	0.1033	0.39172	0.99297	0.93669	0.64493	0.36881	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2023-01-31	Undetermined	Undetermined	Heart	Cardiovascular System
73970	73970	SRR23291013	SRX19234271	SRS16638729	SRP420309	PRJNA929990	Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration	GSE224156	Other	Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.		pubmed:37200435	zfCM 7dpi 2	GSM7016811	source name:Heart\|tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi\|geo loc name:missing\|collection date:missing	zfCM 7dpi 2	Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.	Heart	Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.		tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi	GSM7016811	GSM7016811: zfCM 7dpi 2; Danio rerio; RNA Seq	GSM7016811 r1	GSM7016811	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP420309		HUB-DB-005_HNWVVBGX9_S4_L004_R1_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L004_R2_001.fastq.gz	fastq fastq	692573136.0	8053176.0	GSM7016811 r4	0:26 1:60	A:182418113;C:126757471;G:143869511;T:239393143;N:134898	26	60	182418113	126757471	143869511	239393143	134898	SRX19234271	SRS16638729	SRA1583767	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	2	0.10826	0.81364	0.10182	0.40464	0.9931	0.94034	0.66059	0.40686	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2023-01-31	Undetermined	Undetermined	Heart	Cardiovascular System
73971	73971	SRR23291015	SRX19234270	SRS16638728	SRP420309	PRJNA929990	Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration	GSE224156	Other	Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.		pubmed:37200435	zfCM 7dpi 1	GSM7016810	source name:Heart\|tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi\|geo loc name:missing\|collection date:missing	zfCM 7dpi 1	Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.	Heart	Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.		tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi	GSM7016810	GSM7016810: zfCM 7dpi 1; Danio rerio; RNA Seq	GSM7016810 r1	GSM7016810	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP420309		HUB-DB-001_AHVKTGBGX7_S5_L001_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L001_R2_001.fastq.gz	fastq fastq	471703034.0	5484919.0	GSM7016810 r1	0:26 1:60	A:125045012;C:89627491;G:85413855;T:171466861;N:149815	26	60	125045012	89627491	85413855	171466861	149815	SRX19234270	SRS16638728	SRA1583767	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	2	0.10906	0.67997	0.10214	0.30398	0.99117	0.94209	0.6357	0.45559	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2023-01-31	Undetermined	Undetermined	Heart	Cardiovascular System
73972	73972	SRR23291016	SRX19234270	SRS16638728	SRP420309	PRJNA929990	Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration	GSE224156	Other	Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.		pubmed:37200435	zfCM 7dpi 1	GSM7016810	source name:Heart\|tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi\|geo loc name:missing\|collection date:missing	zfCM 7dpi 1	Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.	Heart	Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.		tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi	GSM7016810	GSM7016810: zfCM 7dpi 1; Danio rerio; RNA Seq	GSM7016810 r1	GSM7016810	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP420309		HUB-DB-001_AHVKTGBGX7_S5_L002_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L002_R2_001.fastq.gz	fastq fastq	489372938.0	5690383.0	GSM7016810 r2	0:26 1:60	A:131516821;C:92202683;G:88685608;T:176824985;N:142841	26	60	131516821	92202683	88685608	176824985	142841	SRX19234270	SRS16638728	SRA1583767	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	2	0.11042	0.68087	0.10314	0.3043	0.99145	0.94882	0.5723	0.46048	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2023-01-31	Undetermined	Undetermined	Heart	Cardiovascular System
73973	73973	SRR23291017	SRX19234270	SRS16638728	SRP420309	PRJNA929990	Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration	GSE224156	Other	Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.		pubmed:37200435	zfCM 7dpi 1	GSM7016810	source name:Heart\|tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi\|geo loc name:missing\|collection date:missing	zfCM 7dpi 1	Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.	Heart	Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.		tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi	GSM7016810	GSM7016810: zfCM 7dpi 1; Danio rerio; RNA Seq	GSM7016810 r1	GSM7016810	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP420309		HUB-DB-001_AHVKTGBGX7_S5_L003_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L003_R2_001.fastq.gz	fastq fastq	407735288.0	4741108.0	GSM7016810 r3	0:26 1:60	A:108841476;C:77418215;G:73171345;T:148203998;N:100254	26	60	108841476	77418215	73171345	148203998	100254	SRX19234270	SRS16638728	SRA1583767	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	2	0.10889	0.67068	0.10168	0.29526	0.99117	0.9471	0.66379	0.42801	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2023-01-31	Undetermined	Undetermined	Heart	Cardiovascular System
73974	73974	SRR23291018	SRX19234270	SRS16638728	SRP420309	PRJNA929990	Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration	GSE224156	Other	Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control.		pubmed:37200435	zfCM 7dpi 1	GSM7016810	source name:Heart\|tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi\|geo loc name:missing\|collection date:missing	zfCM 7dpi 1	Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads.	Heart	Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer.	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.		tissue:Heart\|cell line:NA\|cell type:cardiomyocyte\|genotype:Tgnppa:mCitrine\|treatment:7dpi	GSM7016810	GSM7016810: zfCM 7dpi 1; Danio rerio; RNA Seq	GSM7016810 r1	GSM7016810	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP420309		HUB-DB-001_AHVKTGBGX7_S5_L004_R1_001.fastq.gz HUB-DB-001_AHVKTGBGX7_S5_L004_R2_001.fastq.gz	fastq fastq	505539304.0	5878364.0	GSM7016810 r4	0:26 1:60	A:135189083;C:94908231;G:92431583;T:182885125;N:125282	26	60	135189083	94908231	92431583	182885125	125282	SRX19234270	SRS16638728	SRA1583767	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	2	0.10989	0.68603	0.10295	0.30544	0.99119	0.94783	0.65617	0.41933	26	60	T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2023-01-31	Undetermined	Undetermined	Heart	Cardiovascular System

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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");;