metadata: run_metadata: 857 rows where experiment.library_layout = "SINGLE", experiment.platform = "ILLUMINA" and tissue_curation

857 rows where experiment.library_layout = "SINGLE", experiment.platform = "ILLUMINA" and tissue_curation_coarse = "Cardiovascular System"

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.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	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
5879	5879	ERR1759701	ERX1826022	ERS1474296	ERP020578	PRJEB18632	RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	E-MTAB-5323	Transcriptome Analysis	The aim of this analysis is to uncover novel molecules synthesized and secreted from cardiomyocytes.	ENA FIRST PUBLIC:2016 12 20\|ENA LAST UPDATE:2016 12 15\|ArrayExpress:E MTAB 5323		Protocols: To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.	Sample2	SAMEA27136168	Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute	ENA first public:2016 12 20\|ENA last update:2016 12 15\|External Id:SAMEA27136168\|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|INSDC first public:2016 12 20T17:02:09Z\|INSDC last update:2016 12 15T11:23:10Z\|INSDC status:public\|Submitter Id:E MTAB 5323:Sample2\|broker name:ArrayExpress\|cell type:cardiac myocyte\|common name:zebrafish\|developmental stage:72 hpf\|genotype:Tgmyl7:actn2 tdEodncv44Tg\|sample name:E MTAB 5323:Sample2									Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	E MTAB 5323:Sample2 s	Sample2 s	RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture’s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.	Experimental Factor: Tgmyl7:actn2 tdEodncv44Tg:genotype	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	ERP020578	Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	ENA FIRST PUBLIC:2016 12 20\|ENA LAST UPDATE:2018 11 16	mochizukis_lab_myl7_actn2tdEos_72h_01.fastq.gz	fastq	448234901.0	6016977.0	E MTAB 5323:Sample2	0:74.50 1:0	A:118923409;C:100586009;G:99987046;T:126071553;N:2666884	74	0			118923409	100586009	99987046	126071553	2666884	ERX1826022	ERS1474296	ERA776061	Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|European Nucleotide Archive	Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|European Nucleotide Archive	1	0.88465	0.27583	0.75398	0.55917	75	B	usable mapping rate	illumina	miseq	full_length	poly_a	nebnext	bulk	unknown	unknown	Japan	2016-12-15	Larval	Larval	Heart	Cardiovascular System
5880	5880	ERR1759702	ERX1826022	ERS1474296	ERP020578	PRJEB18632	RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	E-MTAB-5323	Transcriptome Analysis	The aim of this analysis is to uncover novel molecules synthesized and secreted from cardiomyocytes.	ENA FIRST PUBLIC:2016 12 20\|ENA LAST UPDATE:2016 12 15\|ArrayExpress:E MTAB 5323		Protocols: To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.	Sample2	SAMEA27136168	Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute	ENA first public:2016 12 20\|ENA last update:2016 12 15\|External Id:SAMEA27136168\|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|INSDC first public:2016 12 20T17:02:09Z\|INSDC last update:2016 12 15T11:23:10Z\|INSDC status:public\|Submitter Id:E MTAB 5323:Sample2\|broker name:ArrayExpress\|cell type:cardiac myocyte\|common name:zebrafish\|developmental stage:72 hpf\|genotype:Tgmyl7:actn2 tdEodncv44Tg\|sample name:E MTAB 5323:Sample2									Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	E MTAB 5323:Sample2 s	Sample2 s	RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture’s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.	Experimental Factor: Tgmyl7:actn2 tdEodncv44Tg:genotype	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	ERP020578	Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	ENA FIRST PUBLIC:2016 12 20\|ENA LAST UPDATE:2018 11 16	mochizukis_lab_myl7_actn2tdEos_72h_02.fastq.gz	fastq	448116860.0	6016977.0	E MTAB 5323:Sample2 1	0:0 1:74.48	A:127811460;C:99875207;G:106561979;T:113792335;N:75879	0	74			127811460	99875207	106561979	113792335	75879	ERX1826022	ERS1474296	ERA776061	Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|European Nucleotide Archive	Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|European Nucleotide Archive	1	0.91589	0.2509	0.79005	0.54852	75	B	usable mapping rate	illumina	miseq	full_length	poly_a	nebnext	bulk	unknown	unknown	Japan	2016-12-15	Larval	Larval	Heart	Cardiovascular System
5881	5881	ERR1759699	ERX1826021	ERS1474295	ERP020578	PRJEB18632	RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	E-MTAB-5323	Transcriptome Analysis	The aim of this analysis is to uncover novel molecules synthesized and secreted from cardiomyocytes.	ENA FIRST PUBLIC:2016 12 20\|ENA LAST UPDATE:2016 12 15\|ArrayExpress:E MTAB 5323		Protocols: To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.	Sample1	SAMEA27135418	Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute	ENA first public:2016 12 20\|ENA last update:2016 12 15\|External Id:SAMEA27135418\|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|INSDC first public:2016 12 20T17:02:09Z\|INSDC last update:2016 12 15T11:23:10Z\|INSDC status:public\|Submitter Id:E MTAB 5323:Sample1\|broker name:ArrayExpress\|cell type:cardiac myocyte\|common name:zebrafish\|developmental stage:72 hpf\|genotype:Tgmyl7:Nls mCherryncv11Tg\|sample name:E MTAB 5323:Sample1									Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	E MTAB 5323:Sample1 s	Sample1 s	RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture’s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.	Experimental Factor: Tgmyl7:Nls mCherryncv11Tg:genotype	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	ERP020578	Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	ENA FIRST PUBLIC:2016 12 20\|ENA LAST UPDATE:2018 11 16	mochizukis_lab_myl7_NLSmCherry_72h_01.fastq.gz	fastq	766363334.0	10284347.0	E MTAB 5323:Sample1	0:74.52 1:0	A:201960096;C:174999154;G:173403690;T:211341998;N:4658396	74	0			201960096	174999154	173403690	211341998	4658396	ERX1826021	ERS1474295	ERA776061	Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|European Nucleotide Archive	Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|European Nucleotide Archive	1	0.86003	0.20554	0.76301	0.55753	74	B	usable mapping rate	illumina	miseq	full_length	poly_a	nebnext	bulk	unknown	unknown	Japan	2016-12-15	Larval	Larval	Heart	Cardiovascular System
5882	5882	ERR1759700	ERX1826021	ERS1474295	ERP020578	PRJEB18632	RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	E-MTAB-5323	Transcriptome Analysis	The aim of this analysis is to uncover novel molecules synthesized and secreted from cardiomyocytes.	ENA FIRST PUBLIC:2016 12 20\|ENA LAST UPDATE:2016 12 15\|ArrayExpress:E MTAB 5323		Protocols: To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.	Sample1	SAMEA27135418	Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute	ENA first public:2016 12 20\|ENA last update:2016 12 15\|External Id:SAMEA27135418\|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|INSDC first public:2016 12 20T17:02:09Z\|INSDC last update:2016 12 15T11:23:10Z\|INSDC status:public\|Submitter Id:E MTAB 5323:Sample1\|broker name:ArrayExpress\|cell type:cardiac myocyte\|common name:zebrafish\|developmental stage:72 hpf\|genotype:Tgmyl7:Nls mCherryncv11Tg\|sample name:E MTAB 5323:Sample1									Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	E MTAB 5323:Sample1 s	Sample1 s	RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture’s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.	Experimental Factor: Tgmyl7:Nls mCherryncv11Tg:genotype	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	ERP020578	Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	ENA FIRST PUBLIC:2016 12 20\|ENA LAST UPDATE:2018 11 16	mochizukis_lab_myl7_NLSmCHerry_72h_02.fastq.gz	fastq	766251339.0	10284347.0	E MTAB 5323:Sample1 1	0:0 1:74.51	A:214234414;C:174215653;G:180382062;T:197361982;N:57228	0	74			214234414	174215653	180382062	197361982	57228	ERX1826021	ERS1474295	ERA776061	Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|European Nucleotide Archive	Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|European Nucleotide Archive	1	0.87766	0.21561	0.77477	0.53919	73	B	usable mapping rate	illumina	miseq	full_length	poly_a	nebnext	bulk	unknown	unknown	Japan	2016-12-15	Larval	Larval	Heart	Cardiovascular System
10056	10056	ERR4691987	ERX4613068	ERS5216074	ERP124560	PRJEB40865	RNA seq of zebrafish adult MCU mutant hearts	ena-STUDY-UCLA-16-10-2020-22:30:44:295-390	Other	We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity but exhibits cardiac function and structure defects. We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart.	ENA FIRST PUBLIC:2020 12 10\|ENA LAST UPDATE:2020 10 16			zebrafish adult heart RNA	SAMEA7457891	UCLA	ENA FIRST PUBLIC:2020 12 10T17:06:02Z\|ENA LAST UPDATE:2020 10 16T22:30:48Z\|External Id:SAMEA7457891\|INSDC center name:UCLA\|INSDC first public:2020 12 10T17:06:02Z\|INSDC last update:2020 10 16T22:30:48Z\|INSDC status:public\|Submitter Id:mcu mutant 2\|common name:zebrafish\|dev stage:adult\|sample name:mcu mutant 2\|scientific name:Danio rerio\|tissue type:heart									Illumina HiSeq 3000 sequencing	ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 4	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 3000	ERP124560	Illumina HiSeq 3000 sequencing	ENA FIRST PUBLIC:2020 12 10\|ENA LAST UPDATE:2020 10 21	MCU_2.fastq.gz	fastq	1291626898.0	35072619.0	ena RUN UCLA 16 10 2020 22:30:43:819 4	0:36.83 1:0	A:364596432;C:305716590;G:295397140;T:324498501;N:1418235	36	0			364596432	305716590	295397140	324498501	1418235	ERX4613068	ERS5216074	ERA2987364	European Nucleotide Archive	University of California, Los Angeles, USA	1	0.93311	0.08182	0.75852	0.54813	37	B	usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2020-10-16	Adult	Adult	Heart	Cardiovascular System
10057	10057	ERR4691986	ERX4613067	ERS5216073	ERP124560	PRJEB40865	RNA seq of zebrafish adult MCU mutant hearts	ena-STUDY-UCLA-16-10-2020-22:30:44:295-390	Other	We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity but exhibits cardiac function and structure defects. We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart.	ENA FIRST PUBLIC:2020 12 10\|ENA LAST UPDATE:2020 10 16			zebrafish adult heart RNA	SAMEA7457890	UCLA	ENA FIRST PUBLIC:2020 12 10T17:06:02Z\|ENA LAST UPDATE:2020 10 16T22:30:48Z\|External Id:SAMEA7457890\|INSDC center name:UCLA\|INSDC first public:2020 12 10T17:06:02Z\|INSDC last update:2020 10 16T22:30:48Z\|INSDC status:public\|Submitter Id:mcu mutant 1\|common name:zebrafish\|dev stage:adult\|sample name:mcu mutant 1\|scientific name:Danio rerio\|tissue type:heart									Illumina HiSeq 3000 sequencing	ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 3	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 3000	ERP124560	Illumina HiSeq 3000 sequencing	ENA FIRST PUBLIC:2020 12 10\|ENA LAST UPDATE:2020 10 21	MCU_1.fastq.gz	fastq	1236033124.0	33559740.0	ena RUN UCLA 16 10 2020 22:30:43:819 3	0:36.83 1:0	A:348518065;C:293502111;G:279181983;T:313506799;N:1324166	36	0			348518065	293502111	279181983	313506799	1324166	ERX4613067	ERS5216073	ERA2987364	European Nucleotide Archive	University of California, Los Angeles, USA	1	0.92798	0.07907	0.7697	0.5488	37	B	usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2020-10-16	Adult	Adult	Heart	Cardiovascular System
10058	10058	ERR4691985	ERX4613066	ERS5216072	ERP124560	PRJEB40865	RNA seq of zebrafish adult MCU mutant hearts	ena-STUDY-UCLA-16-10-2020-22:30:44:295-390	Other	We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity but exhibits cardiac function and structure defects. We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart.	ENA FIRST PUBLIC:2020 12 10\|ENA LAST UPDATE:2020 10 16			zebrafish adult heart RNA	SAMEA7457889	UCLA	ENA FIRST PUBLIC:2020 12 10T17:06:02Z\|ENA LAST UPDATE:2020 10 16T22:30:48Z\|External Id:SAMEA7457889\|INSDC center name:UCLA\|INSDC first public:2020 12 10T17:06:02Z\|INSDC last update:2020 10 16T22:30:48Z\|INSDC status:public\|Submitter Id:wildtype 2\|common name:zebrafish\|dev stage:adult\|sample name:wildtype 2\|scientific name:Danio rerio\|tissue type:heart									Illumina HiSeq 3000 sequencing	ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 2	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 3000	ERP124560	Illumina HiSeq 3000 sequencing	ENA FIRST PUBLIC:2020 12 10\|ENA LAST UPDATE:2020 10 21	WT_2.fastq.gz	fastq	1180831209.0	32069533.0	ena RUN UCLA 16 10 2020 22:30:43:819 2	0:36.82 1:0	A:328604642;C:281065336;G:278743466;T:291039015;N:1378750	36	0			328604642	281065336	278743466	291039015	1378750	ERX4613066	ERS5216072	ERA2987364	European Nucleotide Archive	University of California, Los Angeles, USA	1	0.92319	0.08946	0.75706	0.49996	37	B	usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2020-10-16	Adult	Adult	Heart	Cardiovascular System
10059	10059	ERR4691984	ERX4613065	ERS5216071	ERP124560	PRJEB40865	RNA seq of zebrafish adult MCU mutant hearts	ena-STUDY-UCLA-16-10-2020-22:30:44:295-390	Other	We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity but exhibits cardiac function and structure defects. We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart.	ENA FIRST PUBLIC:2020 12 10\|ENA LAST UPDATE:2020 10 16			zebrafish adult heart RNA	SAMEA7457888	UCLA	ENA FIRST PUBLIC:2020 12 10T17:06:02Z\|ENA LAST UPDATE:2020 10 16T22:30:48Z\|External Id:SAMEA7457888\|INSDC center name:UCLA\|INSDC first public:2020 12 10T17:06:02Z\|INSDC last update:2020 10 16T22:30:48Z\|INSDC status:public\|Submitter Id:wildtype 1\|common name:zebrafish\|dev stage:adult\|sample name:wildtype 1\|scientific name:Danio rerio\|tissue type:heart									Illumina HiSeq 3000 sequencing	ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 1	unspecified	1			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 3000	ERP124560	Illumina HiSeq 3000 sequencing	ENA FIRST PUBLIC:2020 12 10\|ENA LAST UPDATE:2020 10 21	WT_1.fastq.gz	fastq	1428414407.0	38793098.0	ena RUN UCLA 16 10 2020 22:30:43:819 1	0:36.82 1:0	A:398925739;C:338731211;G:333527196;T:355553981;N:1676280	36	0			398925739	338731211	333527196	355553981	1676280	ERX4613065	ERS5216071	ERA2987364	European Nucleotide Archive	University of California, Los Angeles, USA	1	0.92407	0.08758	0.75726	0.4969	37	B	usable mapping rate	illumina	hiseq_era	unknown	unknown	unknown	bulk	unknown	unknown	United States	2020-10-16	Adult	Adult	Heart	Cardiovascular System
11017	11017	ERR9750937	ERX9298876	ERS12023662	ERP137743	PRJEB52989	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E-MTAB-10643	Transcriptome Analysis	Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells.	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20		Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Expt 2 Uninjured	SAMEA14418104	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.	ENA first public:2022 05 20\|ENA last update:2022 05 20\|External Id:SAMEA14418104\|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC first public:2022 05 20T16:17:49Z\|INSDC last update:2022 05 20T16:17:49Z\|INSDC status:public\|Submitter Id:E MTAB 10643:Expt 2 Uninjured\|age:6\|broker name:ArrayExpress\|cell type:interstitial cell\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|organism part:heart\|sample name:E MTAB 10643:Expt 2 Uninjured\|sex:male\|strain:AB									Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E MTAB 10643:Expt 2 Uninjured p	Expt 2 Uninjured p	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	Zebrafish were euthanized in tricaine and hearts were extracted in PBS "Hearts were pooled and ""pre digested"" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum." The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Experimental Factor: injury:n1\|Experimental Factor: treatment:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP137743	Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20	E2_Uninjured_S2_L002_I1_001.fastq.gz E2_Uninjured_S2_L002_I2_001.fastq.gz E2_Uninjured_S2_L002_R1_001.fastq.gz E2_Uninjured_S2_L002_R2_001.fastq.gz	fastq fastq fastq fastq	9325673775.0	69079065.0	E MTAB 10643:Expt 2 Uninjured	0:10 1:10 2:28 3:87	A:1619571910;C:1420805235;G:1471531128;T:1496998088;N:972294	10	10	28	87	1619571910	1420805235	1471531128	1496998088	972294	ERX9298876	ERS12023662	ERA14538536	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	1	0.93798	0.11364	0.84843	0.53531	87	B	usable mapping rate	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	France	2022-05-20	Adult	Adult	Heart	Cardiovascular System
11018	11018	ERR9750936	ERX9298875	ERS12023661	ERP137743	PRJEB52989	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E-MTAB-10643	Transcriptome Analysis	Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells.	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20		Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Expt 2 Sham	SAMEA14418103	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.	ENA first public:2022 05 20\|ENA last update:2022 05 20\|External Id:SAMEA14418103\|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC first public:2022 05 20T16:17:49Z\|INSDC last update:2022 05 20T16:17:49Z\|INSDC status:public\|Submitter Id:E MTAB 10643:Expt 2 Sham\|age:6\|broker name:ArrayExpress\|cell type:interstitial cell\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:sham surgery\|organism part:heart\|sample name:E MTAB 10643:Expt 2 Sham\|sex:male\|strain:AB									Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E MTAB 10643:Expt 2 Sham p	Expt 2 Sham p	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	Zebrafish were euthanized in tricaine and hearts were extracted in PBS "Hearts were pooled and ""pre digested"" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum." The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Experimental Factor: injury:sham surgery\|Experimental Factor: time:3\|Experimental Factor: treatment:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP137743	Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20	E2_Sham_S1_L002_I1_001.fastq.gz E2_Sham_S1_L002_I2_001.fastq.gz E2_Sham_S1_L002_R1_001.fastq.gz E2_Sham_S1_L002_R2_001.fastq.gz	fastq fastq fastq fastq	11328674040.0	83916104.0	E MTAB 10643:Expt 2 Sham	0:10 1:10 2:28 3:87	A:1955327720;C:1746332187;G:1777122701;T:1820705338;N:1213102	10	10	28	87	1955327720	1746332187	1777122701	1820705338	1213102	ERX9298875	ERS12023661	ERA14538536	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	1	0.92847	0.09981	0.85707	0.46947	87	B	usable mapping rate	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	France	2022-05-20	Adult	Adult	Heart	Cardiovascular System
11019	11019	ERR9750935	ERX9298874	ERS12023660	ERP137743	PRJEB52989	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E-MTAB-10643	Transcriptome Analysis	Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells.	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20		Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Expt 2 3d post amputation	SAMEA14418102	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.	ENA first public:2022 05 20\|ENA last update:2022 05 20\|External Id:SAMEA14418102\|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC first public:2022 05 20T16:17:49Z\|INSDC last update:2022 05 20T16:17:49Z\|INSDC status:public\|Submitter Id:E MTAB 10643:Expt 2 3d post amputation\|age:6\|broker name:ArrayExpress\|cell type:interstitial cell\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:20 percent removal of the cardiac ventricle apex\|organism part:heart\|sample name:E MTAB 10643:Expt 2 3d post amputation\|sex:male\|strain:AB									Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E MTAB 10643:Expt 2 3d post amputation p	Expt 2 3d post amputation p	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	Zebrafish were euthanized in tricaine and hearts were extracted in PBS "Hearts were pooled and ""pre digested"" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum." The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Experimental Factor: injury:20 percent removal of the cardiac ventricle apex\|Experimental Factor: time:3\|Experimental Factor: treatment:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP137743	Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20	E2_3dpa_S3_L002_I1_001.fastq.gz E2_3dpa_S3_L002_I2_001.fastq.gz E2_3dpa_S3_L002_R1_001.fastq.gz E2_3dpa_S3_L002_R2_001.fastq.gz	fastq fastq fastq fastq	16111486440.0	119344344.0	E MTAB 10643:Expt 2 3d post amputation	0:10 1:10 2:28 3:87	A:2610144058;C:2617445332;G:2496763759;T:2656876552;N:1728227	10	10	28	87	2610144058	2617445332	2496763759	2656876552	1728227	ERX9298874	ERS12023660	ERA14538536	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	1	0.94868	0.07071	0.89221	0.54333	87	B	usable mapping rate	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	France	2022-05-20	Adult	Adult	Heart	Cardiovascular System
11020	11020	ERR9750934	ERX9298873	ERS12023659	ERP137743	PRJEB52989	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E-MTAB-10643	Transcriptome Analysis	Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells.	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20		Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Expt 3 3d post amputation + MMP inhibitor	SAMEA14418101	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.	ENA first public:2022 05 20\|ENA last update:2022 05 20\|External Id:SAMEA14418101\|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC first public:2022 05 20T16:17:49Z\|INSDC last update:2022 05 20T16:17:49Z\|INSDC status:public\|Submitter Id:E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor\|age:6\|broker name:ArrayExpress\|cell type:interstitial cell\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:20 percent removal of the cardiac ventricle apex\|organism part:heart\|sample name:E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor\|sex:male\|strain:AB\|treatment:matrix metalloproteinase inhibitor									Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor p	Expt 3 3d post amputation + MMP inhibitor p	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	Zebrafish were euthanized in tricaine and hearts were extracted in PBS "Hearts were pooled and ""pre digested"" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum." The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Experimental Factor: injury:20 percent removal of the cardiac ventricle apex\|Experimental Factor: time:3\|Experimental Factor: treatment:matrix metalloproteinase inhibitor	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP137743	Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20	E2_3dpa_inhibitor_S4_L002_I1_001.fastq.gz E2_3dpa_inhibitor_S4_L002_I2_001.fastq.gz E2_3dpa_inhibitor_S4_L002_R1_001.fastq.gz E2_3dpa_inhibitor_S4_L002_R2_001.fastq.gz	fastq fastq fastq fastq	8621019270.0	63859402.0	E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor	0:10 1:10 2:28 3:87	A:1438763050;C:1365497247;G:1350808021;T:1399773154;N:926502	10	10	28	87	1438763050	1365497247	1350808021	1399773154	926502	ERX9298873	ERS12023659	ERA14538536	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	1	0.92796	0.08671	0.87176	0.55088	87	B	usable mapping rate	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	France	2022-05-20	Adult	Adult	Heart	Cardiovascular System
11021	11021	ERR9750933	ERX9298872	ERS12023658	ERP137743	PRJEB52989	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E-MTAB-10643	Transcriptome Analysis	Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells.	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20		Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Expt 1 Uninjured	SAMEA14418100	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.	ENA first public:2022 05 20\|ENA last update:2022 05 20\|External Id:SAMEA14418100\|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC first public:2022 05 20T16:17:49Z\|INSDC last update:2022 05 20T16:17:49Z\|INSDC status:public\|Submitter Id:E MTAB 10643:Expt 1 Uninjured\|age:6\|broker name:ArrayExpress\|cell type:interstitial cell\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|organism part:heart\|sample name:E MTAB 10643:Expt 1 Uninjured\|sex:male\|strain:AB									Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E MTAB 10643:Expt 1 Uninjured p	Expt 1 Uninjured p	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	Zebrafish were euthanized in tricaine and hearts were extracted in PBS "Hearts were pooled and ""pre digested"" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum." The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Experimental Factor: injury:n1\|Experimental Factor: treatment:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP137743	Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20	E1_Uninjured_S1_L002_I1_001.fastq.gz E1_Uninjured_S1_L002_R1_001.fastq.gz E1_Uninjured_S1_L002_R2_001.fastq.gz	fastq fastq fastq	8575585211.0	67524293.0	E MTAB 10643:Expt 1 Uninjured	0:8 1:28 2:91	A:1801503847;C:1312196506;G:1367890726;T:1663053783;N:65801	8	28	91		1801503847	1312196506	1367890726	1663053783	65801	ERX9298872	ERS12023658	ERA14538536	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	1	0.9169	0.11202	0.81576	0.54253	91	B	usable mapping rate	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	France	2022-05-20	Adult	Adult	Heart	Cardiovascular System
11022	11022	ERR9750932	ERX9298871	ERS12023657	ERP137743	PRJEB52989	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E-MTAB-10643	Transcriptome Analysis	Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells.	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20		Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Expt 1 7d post amputation	SAMEA14418099	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.	ENA first public:2022 05 20\|ENA last update:2022 05 20\|External Id:SAMEA14418099\|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC first public:2022 05 20T16:17:49Z\|INSDC last update:2022 05 20T16:17:49Z\|INSDC status:public\|Submitter Id:E MTAB 10643:Expt 1 7d post amputation\|age:6\|broker name:ArrayExpress\|cell type:interstitial cell\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:20 percent removal of the cardiac ventricle apex\|organism part:heart\|sample name:E MTAB 10643:Expt 1 7d post amputation\|sex:male\|strain:AB									Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E MTAB 10643:Expt 1 7d post amputation p	Expt 1 7d post amputation p	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	Zebrafish were euthanized in tricaine and hearts were extracted in PBS "Hearts were pooled and ""pre digested"" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum." The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Experimental Factor: injury:20 percent removal of the cardiac ventricle apex\|Experimental Factor: time:7\|Experimental Factor: treatment:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP137743	Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20	E1_7d_S3_L002_I1_001.fastq.gz E1_7d_S3_L002_R1_001.fastq.gz E1_7d_S3_L002_R2_001.fastq.gz	fastq fastq fastq	17341796660.0	136549580.0	E MTAB 10643:Expt 1 7d post amputation	0:8 1:28 2:91	A:3506600812;C:2774617588;G:2814960106;T:3329701112;N:132162	8	28	91		3506600812	2774617588	2814960106	3329701112	132162	ERX9298871	ERS12023657	ERA14538536	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	1	0.90616	0.09608	0.82446	0.46632	91	B	usable mapping rate	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	France	2022-05-20	Adult	Adult	Heart	Cardiovascular System
11023	11023	ERR9750931	ERX9298870	ERS12023656	ERP137743	PRJEB52989	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E-MTAB-10643	Transcriptome Analysis	Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells.	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20		Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Expt 1 3d post amputation	SAMEA14418098	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.	ENA first public:2022 05 20\|ENA last update:2022 05 20\|External Id:SAMEA14418098\|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC first public:2022 05 20T16:17:49Z\|INSDC last update:2022 05 20T16:17:49Z\|INSDC status:public\|Submitter Id:E MTAB 10643:Expt 1 3d post amputation\|age:6\|broker name:ArrayExpress\|cell type:interstitial cell\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:20 percent removal of the cardiac ventricle apex\|organism part:heart\|sample name:E MTAB 10643:Expt 1 3d post amputation\|sex:male\|strain:AB									Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E MTAB 10643:Expt 1 3d post amputation p	Expt 1 3d post amputation p	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	Zebrafish were euthanized in tricaine and hearts were extracted in PBS "Hearts were pooled and ""pre digested"" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum." The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Experimental Factor: injury:20 percent removal of the cardiac ventricle apex\|Experimental Factor: time:3\|Experimental Factor: treatment:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP137743	Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20	E1_3d_S2_L002_I1_001.fastq.gz E1_3d_S2_L002_R1_001.fastq.gz E1_3d_S2_L002_R2_001.fastq.gz	fastq fastq fastq	8183008018.0	64433134.0	E MTAB 10643:Expt 1 3d post amputation	0:8 1:28 2:91	A:1630460899;C:1330248096;G:1326144211;T:1576499358;N:62630	8	28	91		1630460899	1330248096	1326144211	1576499358	62630	ERX9298870	ERS12023656	ERA14538536	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	1	0.88759	0.08679	0.82948	0.47863	91	B	usable mapping rate	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	France	2022-05-20	Adult	Adult	Heart	Cardiovascular System
11024	11024	ERR9750930	ERX9298869	ERS12023655	ERP137743	PRJEB52989	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E-MTAB-10643	Transcriptome Analysis	Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells.	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20		Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Expt 1 14d post amputation	SAMEA14418097	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.	ENA first public:2022 05 20\|ENA last update:2022 05 20\|External Id:SAMEA14418097\|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.\|INSDC first public:2022 05 20T16:17:49Z\|INSDC last update:2022 05 20T16:17:49Z\|INSDC status:public\|Submitter Id:E MTAB 10643:Expt 1 14d post amputation\|age:6\|broker name:ArrayExpress\|cell type:interstitial cell\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:20 percent removal of the cardiac ventricle apex\|organism part:heart\|sample name:E MTAB 10643:Expt 1 14d post amputation\|sex:male\|strain:AB									Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	E MTAB 10643:Expt 1 14d post amputation p	Expt 1 14d post amputation p	scRNAseq of post amputation regenerating zebrafish cardiac ventricle	Zebrafish were euthanized in tricaine and hearts were extracted in PBS "Hearts were pooled and ""pre digested"" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum." The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.	Experimental Factor: injury:20 percent removal of the cardiac ventricle apex\|Experimental Factor: time:14\|Experimental Factor: treatment:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP137743	Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle	ENA FIRST PUBLIC:2022 05 20\|ENA LAST UPDATE:2022 05 20	E1_14d_S4_L002_I1_001.fastq.gz E1_14d_S4_L002_R1_001.fastq.gz E1_14d_S4_L002_R2_001.fastq.gz	fastq fastq fastq	12911908390.0	101668570.0	E MTAB 10643:Expt 1 14d post amputation	0:8 1:28 2:91	A:2700371496;C:1971281481;G:2062280628;T:2517806408;N:99857	8	28	91		2700371496	1971281481	2062280628	2517806408	99857	ERX9298869	ERS12023655	ERA14538536	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.\|European Nucleotide Archive	1	0.90771	0.11048	0.81523	0.53024	91	B	usable mapping rate	illumina	novaseq_era	3prime	poly_a	unknown	sc	single_cell_droplet	10x	France	2022-05-20	Adult	Adult	Heart	Cardiovascular System
25170	25170	SRR25661605	SRX21387413	SRS18627977	SRP455520	PRJNA1006302	The transcriptome of hand2 loss and gain of function embryonic cardiomyocytes	GSE241049	Transcriptome Analysis	To gain mechanistic insight into how Hand2 regulates cardiac fusion we performed transcriptomic analyses of hand2 loss and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs each group has 3 replicates.		pubmed:39658721		hand2 FLD+/? 20 hpf CMs rep3	GSM7714404		source name:embryonic heart\|tissue:embryonic heart\|cell type:cardiomyocytes\|genotype:sibling WT of hand2 mutants\|treatment:sorted cells by FACS\|geo loc name:missing\|collection date:missing	hand2 FLD+/? 20 hpf CMs rep3	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59 a maximum Benjamini–Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts	embryonic heart		miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		tissue:embryonic heart\|cell type:cardiomyocytes\|genotype:sibling WT of hand2 mutants\|treatment:sorted cells by FACS	GSM7714404	GSM7714404: hand2 FLD+/? 20 hpf CMs rep3; Danio rerio; RNA Seq	GSM7714404 r1	GSM7714404	1	miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP455520		loader:fastq load.py	E22_3458_Yanli_HT_Lib_WT_het_3_R1.fastq.gz	fastq	2441736984.0	34141777.0	GSM7714404 r1	0:71.52	A:706186414;C:496261994;G:526176364;T:713112212;N:0	71				706186414	496261994	526176364	713112212	0	SRX21387413	SRS18627977	SRA1694205	MPI for heart and lung research	MPI for heart and lung research	1	0.9026	0.15816	0.76278	0.44042	72	B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2023-08-17	Segmentation	Embryo	Heart	Cardiovascular System
25171	25171	SRR25661606	SRX21387412	SRS18627976	SRP455520	PRJNA1006302	The transcriptome of hand2 loss and gain of function embryonic cardiomyocytes	GSE241049	Transcriptome Analysis	To gain mechanistic insight into how Hand2 regulates cardiac fusion we performed transcriptomic analyses of hand2 loss and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs each group has 3 replicates.		pubmed:39658721		hand2 FLD+/? 20 hpf CMs rep2	GSM7714403		source name:embryonic heart\|tissue:embryonic heart\|cell type:cardiomyocytes\|genotype:sibling WT of hand2 mutants\|treatment:sorted cells by FACS\|geo loc name:missing\|collection date:missing	hand2 FLD+/? 20 hpf CMs rep2	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59 a maximum Benjamini–Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts	embryonic heart		miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		tissue:embryonic heart\|cell type:cardiomyocytes\|genotype:sibling WT of hand2 mutants\|treatment:sorted cells by FACS	GSM7714403	GSM7714403: hand2 FLD+/? 20 hpf CMs rep2; Danio rerio; RNA Seq	GSM7714403 r1	GSM7714403	1	miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP455520		loader:fastq load.py	E22_3458_Yanli_HT_Lib_WT_het_2_R1.fastq.gz	fastq	2185611269.0	30558084.0	GSM7714403 r1	0:71.52	A:612617675;C:458632518;G:474458738;T:639902338;N:0	71				612617675	458632518	474458738	639902338	0	SRX21387412	SRS18627976	SRA1694205	MPI for heart and lung research	MPI for heart and lung research	1	0.90042	0.14005	0.75424	0.44277	72	B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2023-08-17	Segmentation	Embryo	Heart	Cardiovascular System
25172	25172	SRR25661607	SRX21387411	SRS18627975	SRP455520	PRJNA1006302	The transcriptome of hand2 loss and gain of function embryonic cardiomyocytes	GSE241049	Transcriptome Analysis	To gain mechanistic insight into how Hand2 regulates cardiac fusion we performed transcriptomic analyses of hand2 loss and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs each group has 3 replicates.		pubmed:39658721		hand2 FLD+/? 20 hpf CMs rep1	GSM7714402		source name:embryonic heart\|tissue:embryonic heart\|cell type:cardiomyocytes\|genotype:sibling WT of hand2 mutants\|treatment:sorted cells by FACS\|geo loc name:missing\|collection date:missing	hand2 FLD+/? 20 hpf CMs rep1	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59 a maximum Benjamini–Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts	embryonic heart		miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		tissue:embryonic heart\|cell type:cardiomyocytes\|genotype:sibling WT of hand2 mutants\|treatment:sorted cells by FACS	GSM7714402	GSM7714402: hand2 FLD+/? 20 hpf CMs rep1; Danio rerio; RNA Seq	GSM7714402 r1	GSM7714402	1	miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP455520		loader:fastq load.py	E22_3458_Yanli_HT_Lib_WT_het_1_R1.fastq.gz	fastq	2291884894.0	32043147.0	GSM7714402 r1	0:71.52	A:635094975;C:489594953;G:499909828;T:667285138;N:0	71				635094975	489594953	499909828	667285138	0	SRX21387411	SRS18627975	SRA1694205	MPI for heart and lung research	MPI for heart and lung research	1	0.90883	0.14288	0.75331	0.44459	71	B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2023-08-17	Segmentation	Embryo	Heart	Cardiovascular System
25173	25173	SRR25661608	SRX21387410	SRS18627974	SRP455520	PRJNA1006302	The transcriptome of hand2 loss and gain of function embryonic cardiomyocytes	GSE241049	Transcriptome Analysis	To gain mechanistic insight into how Hand2 regulates cardiac fusion we performed transcriptomic analyses of hand2 loss and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs each group has 3 replicates.		pubmed:39658721		WT 20 hpf CMs rep3	GSM7714401		source name:embryonic heart\|tissue:embryonic heart\|cell type:cardiomyocytes\|genotype:sibling WT of hand2 OE\|treatment:sorted cells by FACS\|geo loc name:missing\|collection date:missing	WT 20 hpf CMs rep3	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59 a maximum Benjamini–Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts	embryonic heart		miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		tissue:embryonic heart\|cell type:cardiomyocytes\|genotype:sibling WT of hand2 OE\|treatment:sorted cells by FACS	GSM7714401	GSM7714401: WT 20 hpf CMs rep3; Danio rerio; RNA Seq	GSM7714401 r1	GSM7714401	1	miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP455520		loader:fastq load.py	E22_3458_Yanli_HT_Lib_WT_CMs_3_R1.fastq.gz	fastq	2268251602.0	31717610.0	GSM7714401 r1	0:71.51	A:637196241;C:477782543;G:497683941;T:655588877;N:0	71				637196241	477782543	497683941	655588877	0	SRX21387410	SRS18627974	SRA1694205	MPI for heart and lung research	MPI for heart and lung research	1	0.90026	0.13291	0.78707	0.40811	71	B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2023-08-17	Segmentation	Embryo	Heart	Cardiovascular System
25174	25174	SRR25661609	SRX21387409	SRS18627973	SRP455520	PRJNA1006302	The transcriptome of hand2 loss and gain of function embryonic cardiomyocytes	GSE241049	Transcriptome Analysis	To gain mechanistic insight into how Hand2 regulates cardiac fusion we performed transcriptomic analyses of hand2 loss and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs each group has 3 replicates.		pubmed:39658721		WT 20 hpf CMs rep2	GSM7714400		source name:embryonic heart\|tissue:embryonic heart\|cell type:cardiomyocytes\|genotype:sibling WT of hand2 OE\|treatment:sorted cells by FACS\|geo loc name:missing\|collection date:missing	WT 20 hpf CMs rep2	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59 a maximum Benjamini–Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts	embryonic heart		miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		tissue:embryonic heart\|cell type:cardiomyocytes\|genotype:sibling WT of hand2 OE\|treatment:sorted cells by FACS	GSM7714400	GSM7714400: WT 20 hpf CMs rep2; Danio rerio; RNA Seq	GSM7714400 r1	GSM7714400	1	miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP455520		loader:fastq load.py	E22_3458_Yanli_HT_Lib_WT_CMs_2_R1.fastq.gz	fastq	2195524610.0	30700033.0	GSM7714400 r1	0:71.52	A:615401741;C:462686936;G:481135567;T:636300366;N:0	71				615401741	462686936	481135567	636300366	0	SRX21387409	SRS18627973	SRA1694205	MPI for heart and lung research	MPI for heart and lung research	1	0.90323	0.1476	0.78744	0.41728	72	B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2023-08-17	Segmentation	Embryo	Heart	Cardiovascular System
25175	25175	SRR25661610	SRX21387408	SRS18627972	SRP455520	PRJNA1006302	The transcriptome of hand2 loss and gain of function embryonic cardiomyocytes	GSE241049	Transcriptome Analysis	To gain mechanistic insight into how Hand2 regulates cardiac fusion we performed transcriptomic analyses of hand2 loss and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs each group has 3 replicates.		pubmed:39658721		WT 20 hpf CMs rep1	GSM7714399		source name:embryonic heart\|tissue:embryonic heart\|cell type:cardiomyocytes\|genotype:sibling WT of hand2 OE\|treatment:sorted cells by FACS\|geo loc name:missing\|collection date:missing	WT 20 hpf CMs rep1	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59 a maximum Benjamini–Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts	embryonic heart		miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		tissue:embryonic heart\|cell type:cardiomyocytes\|genotype:sibling WT of hand2 OE\|treatment:sorted cells by FACS	GSM7714399	GSM7714399: WT 20 hpf CMs rep1; Danio rerio; RNA Seq	GSM7714399 r1	GSM7714399	1	miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP455520		loader:fastq load.py	E22_3458_Yanli_HT_Lib_WT_CMs_1_R1.fastq.gz	fastq	2258160684.0	31576661.0	GSM7714399 r1	0:71.51	A:641254288;C:471580136;G:491501482;T:653824778;N:0	71				641254288	471580136	491501482	653824778	0	SRX21387408	SRS18627972	SRA1694205	MPI for heart and lung research	MPI for heart and lung research	1	0.9	0.13993	0.78445	0.40575	72	B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2023-08-17	Segmentation	Embryo	Heart	Cardiovascular System
25176	25176	SRR25661611	SRX21387407	SRS18627971	SRP455520	PRJNA1006302	The transcriptome of hand2 loss and gain of function embryonic cardiomyocytes	GSE241049	Transcriptome Analysis	To gain mechanistic insight into how Hand2 regulates cardiac fusion we performed transcriptomic analyses of hand2 loss and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs each group has 3 replicates.		pubmed:39658721		hand2 OE 20 hpf CMs rep3	GSM7714398		source name:embryonic heart\|tissue:embryonic heart\|cell type:cardiomyocytes\|genotype:overexpression hand2 in myocardium\|treatment:sorted cells by FACS\|geo loc name:missing\|collection date:missing	hand2 OE 20 hpf CMs rep3	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59 a maximum Benjamini–Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts	embryonic heart		miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		tissue:embryonic heart\|cell type:cardiomyocytes\|genotype:overexpression hand2 in myocardium\|treatment:sorted cells by FACS	GSM7714398	GSM7714398: hand2 OE 20 hpf CMs rep3; Danio rerio; RNA Seq	GSM7714398 r1	GSM7714398	1	miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP455520		loader:fastq load.py	E22_3458_Yanli_HT_Lib_OE_CMs_3_R1.fastq.gz	fastq	1886569909.0	26380170.0	GSM7714398 r1	0:71.51	A:534874421;C:392168718;G:411533838;T:547992932;N:0	71				534874421	392168718	411533838	547992932	0	SRX21387407	SRS18627971	SRA1694205	MPI for heart and lung research	MPI for heart and lung research	1	0.89968	0.14763	0.77881	0.42601	72	B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2023-08-17	Segmentation	Embryo	Heart	Cardiovascular System
25177	25177	SRR25661612	SRX21387406	SRS18627970	SRP455520	PRJNA1006302	The transcriptome of hand2 loss and gain of function embryonic cardiomyocytes	GSE241049	Transcriptome Analysis	To gain mechanistic insight into how Hand2 regulates cardiac fusion we performed transcriptomic analyses of hand2 loss and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs each group has 3 replicates.		pubmed:39658721		hand2 OE 20 hpf CMs rep2	GSM7714397		source name:embryonic heart\|tissue:embryonic heart\|cell type:cardiomyocytes\|genotype:overexpression hand2 in myocardium\|treatment:sorted cells by FACS\|geo loc name:missing\|collection date:missing	hand2 OE 20 hpf CMs rep2	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59 a maximum Benjamini–Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts	embryonic heart		miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		tissue:embryonic heart\|cell type:cardiomyocytes\|genotype:overexpression hand2 in myocardium\|treatment:sorted cells by FACS	GSM7714397	GSM7714397: hand2 OE 20 hpf CMs rep2; Danio rerio; RNA Seq	GSM7714397 r1	GSM7714397	1	miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP455520		loader:fastq load.py	E22_3458_Yanli_HT_Lib_OE_CMs_2_R1.fastq.gz	fastq	2197151812.0	30722639.0	GSM7714397 r1	0:71.52	A:617116635;C:461951919;G:481371246;T:636712012;N:0	71				617116635	461951919	481371246	636712012	0	SRX21387406	SRS18627970	SRA1694205	MPI for heart and lung research	MPI for heart and lung research	1	0.90877	0.14744	0.77191	0.42845	72	B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2023-08-17	Segmentation	Embryo	Heart	Cardiovascular System
25178	25178	SRR25661613	SRX21387405	SRS18627969	SRP455520	PRJNA1006302	The transcriptome of hand2 loss and gain of function embryonic cardiomyocytes	GSE241049	Transcriptome Analysis	To gain mechanistic insight into how Hand2 regulates cardiac fusion we performed transcriptomic analyses of hand2 loss and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs each group has 3 replicates.		pubmed:39658721		hand2 OE 20 hpf CMs rep1	GSM7714396		source name:embryonic heart\|tissue:embryonic heart\|cell type:cardiomyocytes\|genotype:overexpression hand2 in myocardium\|treatment:sorted cells by FACS\|geo loc name:missing\|collection date:missing	hand2 OE 20 hpf CMs rep1	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59 a maximum Benjamini–Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts	embryonic heart		miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		tissue:embryonic heart\|cell type:cardiomyocytes\|genotype:overexpression hand2 in myocardium\|treatment:sorted cells by FACS	GSM7714396	GSM7714396: hand2 OE 20 hpf CMs rep1; Danio rerio; RNA Seq	GSM7714396 r1	GSM7714396	1	miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP455520		loader:fastq load.py	E22_3458_Yanli_HT_Lib_OE_CMs_1_R1.fastq.gz	fastq	1773398936.0	24797998.0	GSM7714396 r1	0:71.51	A:495618212;C:375438077;G:390377060;T:511965587;N:0	71				495618212	375438077	390377060	511965587	0	SRX21387405	SRS18627969	SRA1694205	MPI for heart and lung research	MPI for heart and lung research	1	0.90769	0.1387	0.7768	0.42096	72	B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2023-08-17	Segmentation	Embryo	Heart	Cardiovascular System
25179	25179	SRR25661614	SRX21387404	SRS18627968	SRP455520	PRJNA1006302	The transcriptome of hand2 loss and gain of function embryonic cardiomyocytes	GSE241049	Transcriptome Analysis	To gain mechanistic insight into how Hand2 regulates cardiac fusion we performed transcriptomic analyses of hand2 loss and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs each group has 3 replicates.		pubmed:39658721		hand2 FLD / 20 hpf CMs rep3	GSM7714395		source name:embryonic heart\|tissue:embryonic heart\|cell type:cardiomyocytes\|genotype:hand2 mutant\|treatment:sorted cells by FACS\|geo loc name:missing\|collection date:missing	hand2 FLD / 20 hpf CMs rep3	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59 a maximum Benjamini–Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts	embryonic heart		miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		tissue:embryonic heart\|cell type:cardiomyocytes\|genotype:hand2 mutant\|treatment:sorted cells by FACS	GSM7714395	GSM7714395: hand2 FLD / 20 hpf CMs rep3; Danio rerio; RNA Seq	GSM7714395 r1	GSM7714395	1	miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP455520		loader:fastq load.py	E22_3458_Yanli_HT_Lib_Mut_3_R1.fastq.gz	fastq	2179400259.0	30471965.0	GSM7714395 r1	0:71.52	A:600555691;C:468535203;G:483122661;T:627186704;N:0	71				600555691	468535203	483122661	627186704	0	SRX21387404	SRS18627968	SRA1694205	MPI for heart and lung research	MPI for heart and lung research	1	0.91581	0.12256	0.75209	0.43413	71	B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2023-08-17	Segmentation	Embryo	Heart	Cardiovascular System
25180	25180	SRR25661615	SRX21387403	SRS18627967	SRP455520	PRJNA1006302	The transcriptome of hand2 loss and gain of function embryonic cardiomyocytes	GSE241049	Transcriptome Analysis	To gain mechanistic insight into how Hand2 regulates cardiac fusion we performed transcriptomic analyses of hand2 loss and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs each group has 3 replicates.		pubmed:39658721		hand2 FLD / 20 hpf CMs rep2	GSM7714394		source name:embryonic heart\|tissue:embryonic heart\|cell type:cardiomyocytes\|genotype:hand2 mutant\|treatment:sorted cells by FACS\|geo loc name:missing\|collection date:missing	hand2 FLD / 20 hpf CMs rep2	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59 a maximum Benjamini–Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts	embryonic heart		miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		tissue:embryonic heart\|cell type:cardiomyocytes\|genotype:hand2 mutant\|treatment:sorted cells by FACS	GSM7714394	GSM7714394: hand2 FLD / 20 hpf CMs rep2; Danio rerio; RNA Seq	GSM7714394 r1	GSM7714394	1	miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP455520		loader:fastq load.py	E22_3458_Yanli_HT_Lib_Mut_2_R1.fastq.gz	fastq	2340991168.0	32733068.0	GSM7714394 r1	0:71.52	A:647423337;C:500120073;G:514803152;T:678644606;N:0	71				647423337	500120073	514803152	678644606	0	SRX21387403	SRS18627967	SRA1694205	MPI for heart and lung research	MPI for heart and lung research	1	0.91231	0.12561	0.75118	0.44445	71	B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2023-08-17	Segmentation	Embryo	Heart	Cardiovascular System
25181	25181	SRR25661616	SRX21387402	SRS18627966	SRP455520	PRJNA1006302	The transcriptome of hand2 loss and gain of function embryonic cardiomyocytes	GSE241049	Transcriptome Analysis	To gain mechanistic insight into how Hand2 regulates cardiac fusion we performed transcriptomic analyses of hand2 loss and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs each group has 3 replicates.		pubmed:39658721		hand2 FLD / 20 hpf CMs rep1	GSM7714393		source name:embryonic heart\|tissue:embryonic heart\|cell type:cardiomyocytes\|genotype:hand2 mutant\|treatment:sorted cells by FACS\|geo loc name:missing\|collection date:missing	hand2 FLD / 20 hpf CMs rep1	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59 a maximum Benjamini–Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts	embryonic heart		miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		tissue:embryonic heart\|cell type:cardiomyocytes\|genotype:hand2 mutant\|treatment:sorted cells by FACS	GSM7714393	GSM7714393: hand2 FLD / 20 hpf CMs rep1; Danio rerio; RNA Seq	GSM7714393 r1	GSM7714393	1	miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP455520		loader:fastq load.py	E22_3458_Yanli_HT_Lib_Mut_1_R1.fastq.gz	fastq	2727863036.0	38140997.0	GSM7714393 r1	0:71.52	A:760867462;C:577539041;G:596986102;T:792470431;N:0	71				760867462	577539041	596986102	792470431	0	SRX21387402	SRS18627966	SRA1694205	MPI for heart and lung research	MPI for heart and lung research	1	0.91175	0.1342	0.75282	0.44063	72	B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2023-08-17	Segmentation	Embryo	Heart	Cardiovascular System
25196	25196	SRR25685540	SRX21410747	SRS18649229	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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 overexpression sample 4	GSM7717538		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	Hmga1a overexpression sample 4	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717538	GSM7717538: Hmga1a overexpression sample 4; Danio rerio; RNA Seq	GSM7717538 r1	GSM7717538	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L001_OE4_cbc.fastq.gz	fastq	373009260.0	6216821.0	GSM7717538 r1	0:60	A:154344754;C:67291339;G:55785796;T:95519920;N:67451	60				154344754	67291339	55785796	95519920	67451	SRX21410747	SRS18649229	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.89552	0.06993	0.9276	0.58138	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25197	25197	SRR25685541	SRX21410747	SRS18649229	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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 overexpression sample 4	GSM7717538		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	Hmga1a overexpression sample 4	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717538	GSM7717538: Hmga1a overexpression sample 4; Danio rerio; RNA Seq	GSM7717538 r1	GSM7717538	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L002_OE4_cbc.fastq.gz	fastq	362301060.0	6038351.0	GSM7717538 r2	0:60	A:106180158;C:75387781;G:73886850;T:106761396;N:84875	60				106180158	75387781	73886850	106761396	84875	SRX21410747	SRS18649229	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.89159	0.06701	0.87081	0.62237	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25198	25198	SRR25685542	SRX21410747	SRS18649229	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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 overexpression sample 4	GSM7717538		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	Hmga1a overexpression sample 4	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717538	GSM7717538: Hmga1a overexpression sample 4; Danio rerio; RNA Seq	GSM7717538 r1	GSM7717538	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L003_OE4_cbc.fastq.gz	fastq	384538200.0	6408970.0	GSM7717538 r3	0:60	A:113163070;C:80510291;G:76775008;T:114062728;N:27103	60				113163070	80510291	76775008	114062728	27103	SRX21410747	SRS18649229	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.90032	0.06985	0.87008	0.61631	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25199	25199	SRR25685543	SRX21410747	SRS18649229	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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 overexpression sample 4	GSM7717538		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	Hmga1a overexpression sample 4	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717538	GSM7717538: Hmga1a overexpression sample 4; Danio rerio; RNA Seq	GSM7717538 r1	GSM7717538	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L004_OE4_cbc.fastq.gz	fastq	369674700.0	6161245.0	GSM7717538 r4	0:60	A:108130666;C:76988468;G:75491768;T:109027980;N:35818	60				108130666	76988468	75491768	109027980	35818	SRX21410747	SRS18649229	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.89622	0.06895	0.86854	0.61464	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25200	25200	SRR25685544	SRX21410746	SRS18649228	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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 overexpression sample 3	GSM7717537		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	Hmga1a overexpression sample 3	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717537	GSM7717537: Hmga1a overexpression sample 3; Danio rerio; RNA Seq	GSM7717537 r1	GSM7717537	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L001_OE3_cbc.fastq.gz	fastq	172977180.0	2882953.0	GSM7717537 r1	0:60	A:75387211;C:31808233;G:24071421;T:41679068;N:31247	60				75387211	31808233	24071421	41679068	31247	SRX21410746	SRS18649228	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.88458	0.06987	0.92788	0.58263	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25201	25201	SRR25685545	SRX21410746	SRS18649228	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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 overexpression sample 3	GSM7717537		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	Hmga1a overexpression sample 3	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717537	GSM7717537: Hmga1a overexpression sample 3; Danio rerio; RNA Seq	GSM7717537 r1	GSM7717537	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L002_OE3_cbc.fastq.gz	fastq	168370020.0	2806167.0	GSM7717537 r2	0:60	A:49447288;C:35622124;G:34182575;T:49078813;N:39220	60				49447288	35622124	34182575	49078813	39220	SRX21410746	SRS18649228	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.88366	0.06639	0.87519	0.43134	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25202	25202	SRR25685546	SRX21410746	SRS18649228	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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 overexpression sample 3	GSM7717537		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	Hmga1a overexpression sample 3	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717537	GSM7717537: Hmga1a overexpression sample 3; Danio rerio; RNA Seq	GSM7717537 r1	GSM7717537	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L003_OE3_cbc.fastq.gz	fastq	177341340.0	2955689.0	GSM7717537 r3	0:60	A:52304623;C:37759158;G:35264433;T:52000964;N:12162	60				52304623	37759158	35264433	52000964	12162	SRX21410746	SRS18649228	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.8907	0.06795	0.87405	0.57596	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25203	25203	SRR25685547	SRX21410746	SRS18649228	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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 overexpression sample 3	GSM7717537		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	Hmga1a overexpression sample 3	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717537	GSM7717537: Hmga1a overexpression sample 3; Danio rerio; RNA Seq	GSM7717537 r1	GSM7717537	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L004_OE3_cbc.fastq.gz	fastq	172482600.0	2874710.0	GSM7717537 r4	0:60	A:50610545;C:36521080;G:35043934;T:50291237;N:15804	60				50610545	36521080	35043934	50291237	15804	SRX21410746	SRS18649228	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.88558	0.06686	0.87373	0.57425	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25204	25204	SRR25685548	SRX21410745	SRS18649227	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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 overexpression sample 2	GSM7717536		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	Hmga1a overexpression sample 2	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717536	GSM7717536: Hmga1a overexpression sample 2; Danio rerio; RNA Seq	GSM7717536 r1	GSM7717536	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L001_OE2_cbc.fastq.gz	fastq	420273960.0	7004566.0	GSM7717536 r1	0:60	A:172608345;C:77102289;G:65053968;T:105434207;N:75151	60				172608345	77102289	65053968	105434207	75151	SRX21410745	SRS18649227	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.90654	0.06306	0.92904	0.38886	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25205	25205	SRR25685549	SRX21410745	SRS18649227	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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 overexpression sample 2	GSM7717536		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	Hmga1a overexpression sample 2	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717536	GSM7717536: Hmga1a overexpression sample 2; Danio rerio; RNA Seq	GSM7717536 r1	GSM7717536	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L002_OE2_cbc.fastq.gz	fastq	408658800.0	6810980.0	GSM7717536 r2	0:60	A:118741152;C:85204554;G:86928543;T:117687807;N:96744	60				118741152	85204554	86928543	117687807	96744	SRX21410745	SRS18649227	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.90277	0.06298	0.87302	0.66727	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25206	25206	SRR25685550	SRX21410745	SRS18649227	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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 overexpression sample 2	GSM7717536		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	Hmga1a overexpression sample 2	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717536	GSM7717536: Hmga1a overexpression sample 2; Danio rerio; RNA Seq	GSM7717536 r1	GSM7717536	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L003_OE2_cbc.fastq.gz	fastq	433893360.0	7231556.0	GSM7717536 r3	0:60	A:126666020;C:91068379;G:90449908;T:125677088;N:31965	60				126666020	91068379	90449908	125677088	31965	SRX21410745	SRS18649227	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.90833	0.06364	0.87351	0.66644	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25207	25207	SRR25685551	SRX21410745	SRS18649227	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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 overexpression sample 2	GSM7717536		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	Hmga1a overexpression sample 2	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717536	GSM7717536: Hmga1a overexpression sample 2; Danio rerio; RNA Seq	GSM7717536 r1	GSM7717536	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L004_OE2_cbc.fastq.gz	fastq	418311900.0	6971865.0	GSM7717536 r4	0:60	A:121375806;C:87324728;G:89011817;T:120559021;N:40528	60				121375806	87324728	89011817	120559021	40528	SRX21410745	SRS18649227	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.90583	0.06349	0.87156	0.36876	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25208	25208	SRR25685552	SRX21410744	SRS18649226	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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 overexpression sample 1	GSM7717535		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	Hmga1a overexpression sample 1	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717535	GSM7717535: Hmga1a overexpression sample 1; Danio rerio; RNA Seq	GSM7717535 r1	GSM7717535	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L001_OE1_cbc.fastq.gz	fastq	219019680.0	3650328.0	GSM7717535 r1	0:60	A:89205341;C:39777204;G:33514473;T:56486057;N:36605	60				89205341	39777204	33514473	56486057	36605	SRX21410744	SRS18649226	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.89316	0.08503	0.92125	0.51486	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25209	25209	SRR25685553	SRX21410744	SRS18649226	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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 overexpression sample 1	GSM7717535		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	Hmga1a overexpression sample 1	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717535	GSM7717535: Hmga1a overexpression sample 1; Danio rerio; RNA Seq	GSM7717535 r1	GSM7717535	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L002_OE1_cbc.fastq.gz	fastq	213035040.0	3550584.0	GSM7717535 r2	0:60	A:60747442;C:44096249;G:44275929;T:63866231;N:49189	60				60747442	44096249	44275929	63866231	49189	SRX21410744	SRS18649226	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.89017	0.08631	0.86543	0.52632	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25210	25210	SRR25685554	SRX21410744	SRS18649226	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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 overexpression sample 1	GSM7717535		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	Hmga1a overexpression sample 1	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717535	GSM7717535: Hmga1a overexpression sample 1; Danio rerio; RNA Seq	GSM7717535 r1	GSM7717535	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L003_OE1_cbc.fastq.gz	fastq	226019460.0	3766991.0	GSM7717535 r3	0:60	A:64732665;C:47081812;G:46018051;T:68171208;N:15724	60				64732665	47081812	46018051	68171208	15724	SRX21410744	SRS18649226	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.89632	0.08716	0.86661	0.54361	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25211	25211	SRR25685555	SRX21410744	SRS18649226	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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 overexpression sample 1	GSM7717535		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	Hmga1a overexpression sample 1	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:Hmga1a overexpression\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717535	GSM7717535: Hmga1a overexpression sample 1; Danio rerio; RNA Seq	GSM7717535 r1	GSM7717535	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L004_OE1_cbc.fastq.gz	fastq	217742460.0	3629041.0	GSM7717535 r4	0:60	A:61973072;C:45113665;G:45294805;T:65339336;N:21582	60				61973072	45113665	45294805	65339336	21582	SRX21410744	SRS18649226	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.89237	0.08517	0.86454	0.54639	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25212	25212	SRR25685556	SRX21410743	SRS18649225	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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		control sample 4	GSM7717534		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	control sample 4	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717534	GSM7717534: control sample 4; Danio rerio; RNA Seq	GSM7717534 r1	GSM7717534	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L001_Ctrl4_cbc.fastq.gz	fastq	242809260.0	4046821.0	GSM7717534 r1	0:60	A:101286554;C:44368173;G:36112695;T:60997635;N:44203	60				101286554	44368173	36112695	60997635	44203	SRX21410743	SRS18649225	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.87519	0.14838	0.9362	0.79824	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25213	25213	SRR25685557	SRX21410743	SRS18649225	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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		control sample 4	GSM7717534		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	control sample 4	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717534	GSM7717534: control sample 4; Danio rerio; RNA Seq	GSM7717534 r1	GSM7717534	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L002_Ctrl4_cbc.fastq.gz	fastq	235587720.0	3926462.0	GSM7717534 r2	0:60	A:71954218;C:50127333;G:45371371;T:68077780;N:57018	60				71954218	50127333	45371371	68077780	57018	SRX21410743	SRS18649225	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.8759	0.14468	0.88075	0.74532	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25214	25214	SRR25685558	SRX21410743	SRS18649225	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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		control sample 4	GSM7717534		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	control sample 4	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717534	GSM7717534: control sample 4; Danio rerio; RNA Seq	GSM7717534 r1	GSM7717534	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L003_Ctrl4_cbc.fastq.gz	fastq	248320680.0	4138678.0	GSM7717534 r3	0:60	A:76188968;C:53138643;G:46699955;T:72274599;N:18515	60				76188968	53138643	46699955	72274599	18515	SRX21410743	SRS18649225	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.88396	0.1471	0.87864	0.74275	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25215	25215	SRR25685559	SRX21410743	SRS18649225	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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		control sample 4	GSM7717534		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	control sample 4	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717534	GSM7717534: control sample 4; Danio rerio; RNA Seq	GSM7717534 r1	GSM7717534	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L004_Ctrl4_cbc.fastq.gz	fastq	239678820.0	3994647.0	GSM7717534 r4	0:60	A:73122694;C:51017089;G:46184519;T:69330703;N:23815	60				73122694	51017089	46184519	69330703	23815	SRX21410743	SRS18649225	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.88113	0.14666	0.88045	0.79921	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25216	25216	SRR25685560	SRX21410742	SRS18649224	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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		control sample 3	GSM7717533		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	control sample 3	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717533	GSM7717533: control sample 3; Danio rerio; RNA Seq	GSM7717533 r1	GSM7717533	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L001_Ctrl3_cbc.fastq.gz	fastq	164862000.0	2747700.0	GSM7717533 r1	0:60	A:67317722;C:30175032;G:25320195;T:42019155;N:29896	60				67317722	30175032	25320195	42019155	29896	SRX21410742	SRS18649224	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.8874	0.16231	0.93513	0.45903	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25217	25217	SRR25685561	SRX21410742	SRS18649224	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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		control sample 3	GSM7717533		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	control sample 3	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717533	GSM7717533: control sample 3; Danio rerio; RNA Seq	GSM7717533 r1	GSM7717533	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L002_Ctrl3_cbc.fastq.gz	fastq	159878880.0	2664648.0	GSM7717533 r2	0:60	A:48277840;C:33800190;G:31556276;T:46206979;N:37595	60				48277840	33800190	31556276	46206979	37595	SRX21410742	SRS18649224	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.8874	0.15941	0.88038	0.79589	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25218	25218	SRR25685562	SRX21410742	SRS18649224	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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		control sample 3	GSM7717533		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	control sample 3	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717533	GSM7717533: control sample 3; Danio rerio; RNA Seq	GSM7717533 r1	GSM7717533	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L003_Ctrl3_cbc.fastq.gz	fastq	169506240.0	2825104.0	GSM7717533 r3	0:60	A:51435401;C:36027782;G:32684721;T:49346338;N:11998	60				51435401	36027782	32684721	49346338	11998	SRX21410742	SRS18649224	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.89554	0.16117	0.87947	0.795	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25219	25219	SRR25685563	SRX21410742	SRS18649224	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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		control sample 3	GSM7717533		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	control sample 3	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717533	GSM7717533: control sample 3; Danio rerio; RNA Seq	GSM7717533 r1	GSM7717533	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L004_Ctrl3_cbc.fastq.gz	fastq	163347840.0	2722464.0	GSM7717533 r4	0:60	A:49253957;C:34538564;G:32268358;T:47272095;N:14866	60				49253957	34538564	32268358	47272095	14866	SRX21410742	SRS18649224	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.89252	0.15956	0.8784	0.79732	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25220	25220	SRR25685564	SRX21410741	SRS18649223	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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		control sample 2	GSM7717532		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	control sample 2	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717532	GSM7717532: control sample 2; Danio rerio; RNA Seq	GSM7717532 r1	GSM7717532	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L001_Ctrl2_cbc.fastq.gz	fastq	19885560.0	331426.0	GSM7717532 r1	0:60	A:8615440;C:3592607;G:2886695;T:4787767;N:3051	60				8615440	3592607	2886695	4787767	3051	SRX21410741	SRS18649223	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.84848	0.13671	0.96136	0.84253	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25221	25221	SRR25685565	SRX21410741	SRS18649223	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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		control sample 2	GSM7717532		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	control sample 2	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717532	GSM7717532: control sample 2; Danio rerio; RNA Seq	GSM7717532 r1	GSM7717532	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L002_Ctrl2_cbc.fastq.gz	fastq	19226760.0	320446.0	GSM7717532 r2	0:60	A:5898378;C:4022375;G:3854218;T:5447181;N:4608	60				5898378	4022375	3854218	5447181	4608	SRX21410741	SRS18649223	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.84542	0.13731	0.94004	0.38758	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25222	25222	SRR25685566	SRX21410741	SRS18649223	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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		control sample 2	GSM7717532		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	control sample 2	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717532	GSM7717532: control sample 2; Danio rerio; RNA Seq	GSM7717532 r1	GSM7717532	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L003_Ctrl2_cbc.fastq.gz	fastq	20360520.0	339342.0	GSM7717532 r3	0:60	A:6273552;C:4289098;G:3982791;T:5813710;N:1369	60				6273552	4289098	3982791	5813710	1369	SRX21410741	SRS18649223	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.85213	0.13819	0.93929	0.83913	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25223	25223	SRR25685567	SRX21410741	SRS18649223	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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		control sample 2	GSM7717532		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	control sample 2	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717532	GSM7717532: control sample 2; Danio rerio; RNA Seq	GSM7717532 r1	GSM7717532	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L004_Ctrl2_cbc.fastq.gz	fastq	19742340.0	329039.0	GSM7717532 r4	0:60	A:6042722;C:4140425;G:3955209;T:5601961;N:2023	60				6042722	4140425	3955209	5601961	2023	SRX21410741	SRS18649223	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.84722	0.13682	0.93933	0.83301	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25224	25224	SRR25685568	SRX21410740	SRS18649222	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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		control sample 1	GSM7717531		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	control sample 1	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717531	GSM7717531: control sample 1; Danio rerio; RNA Seq	GSM7717531 r1	GSM7717531	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L001_Ctrl1_cbc.fastq.gz	fastq	296163420.0	4936057.0	GSM7717531 r1	0:60	A:121966307;C:53233433;G:44972413;T:75936522;N:54745	60				121966307	53233433	44972413	75936522	54745	SRX21410740	SRS18649222	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.88546	0.17055	0.92681	0.76028	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25225	25225	SRR25685569	SRX21410740	SRS18649222	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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		control sample 1	GSM7717531		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	control sample 1	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717531	GSM7717531: control sample 1; Danio rerio; RNA Seq	GSM7717531 r1	GSM7717531	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L002_Ctrl1_cbc.fastq.gz	fastq	287707980.0	4795133.0	GSM7717531 r2	0:60	A:87738683;C:59468794;G:56448494;T:83984130;N:67879	60				87738683	59468794	56448494	83984130	67879	SRX21410740	SRS18649222	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.88284	0.16626	0.86561	0.74308	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25226	25226	SRR25685570	SRX21410740	SRS18649222	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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		control sample 1	GSM7717531		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	control sample 1	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717531	GSM7717531: control sample 1; Danio rerio; RNA Seq	GSM7717531 r1	GSM7717531	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L003_Ctrl1_cbc.fastq.gz	fastq	303833460.0	5063891.0	GSM7717531 r3	0:60	A:93092013;C:63221167;G:58235370;T:89262119;N:22791	60				93092013	63221167	58235370	89262119	22791	SRX21410740	SRS18649222	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.89102	0.16657	0.86336	0.75396	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25227	25227	SRR25685571	SRX21410740	SRS18649222	SRP455779	PRJNA1006658	Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE]	GSE241157	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		control sample 1	GSM7717531		source name:adult heart\|tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen\|geo loc name:missing\|collection date:missing	control sample 1	FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts	adult heart	zebrafish were treated with tamoxifen to induce Hmga1a overexpression	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		tissue:adult heart\|genotype 1:cmlc2:dsred\|genotype 2:control\|cell type:cardiomyocytes\|treatment:14 days post tamoxifen	GSM7717531	GSM7717531: control sample 1; Danio rerio; RNA Seq	GSM7717531 r1	GSM7717531	1	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP455779			HUB-PN-b004_HHHK2BGXN_S1_L004_Ctrl1_cbc.fastq.gz	fastq	293865840.0	4897764.0	GSM7717531 r4	0:60	A:89531768;C:60796725;G:57688758;T:85819485;N:29104	60				89531768	60796725	57688758	85819485	29104	SRX21410740	SRS18649222	SRA1695358	Jeroen Bakkers, Hubrecht Institute	Jeroen Bakkers, Hubrecht Institute	1	0.88911	0.16498	0.86145	0.75653	60	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	Netherlands	2023-08-18	Adult	Adult	Heart	Cardiovascular System
25320	25320	SRR25810878	SRX21533024	SRS18745490	SRP457576	PRJNA1010780	Effect of egr3 knockout on gene expression of dissected zebrafish hearts	GSE241935	Transcriptome Analysis	To screen for Egr3 targets mediating cardiac valve development we assessed gene expression on dissected hearts of egr3 mutants and wild type siblings. Overall design: To evaluate the transcriptional differences underlying the egr3 mutant phenotype we conducted a bulk RNA seq analysis in dissected zebrafish hearts at 48 hpf. We dissected 20 hearts for each biological duplicate of egr3 mutant and wild type sibling samples in cold DMEM with 10% FBS. Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12µl of RNase free water. Analysis of the obtained reads confirmed the 11bp deletion in the mutant samples. 1. Boezio G. L. M. et al. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 16 2023. https://doi.org:10.1242/dmm.049571		pubmed:38748804		egr3 wild type siblings 2	GSM7745909		source name:Heart\|tissue:Heart\|genotype:bns577+/+\|geo loc name:missing\|collection date:missing	egr3 wild type siblings 2	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 2.27.1 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.30.1 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2 and batch corrected using CountClust each biological replicate = one batch Dey K et al. Visualizing the structure of RNA seq expression data using grade of membership models. Genes were classified as significantly differentially expressed at average count > 5 multiple testing adjusted p value < 0.05 and 0.585 < log2FC > 0.585. Assembly: danRer11 Supplementary files format and content: libryr size notmalize amd batch corrected counts	Heart		Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.		tissue:Heart\|genotype:bns577+/+	GSM7745909	GSM7745909: egr3 wild type siblings 2; Danio rerio; RNA Seq	GSM7745909 r1	GSM7745909	1	Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP457576		loader:fastq load.py	E22_3626_Lib_Agatha_egr3_WT2_R1.fastq.gz	fastq	3473319384.0	49279465.0	GSM7745909 r1	0:70.48	A:943794847;C:792135324;G:792042625;T:945083925;N:262663	70				943794847	792135324	792042625	945083925	262663	SRX21533024	SRS18745490	SRA1702458	MPI for heart and lung research	MPI for heart and lung research	1	0.68549	0.04588	0.76865	0.44964	71	B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2023-08-30	Undetermined	Undetermined	Heart	Cardiovascular System
25321	25321	SRR25810879	SRX21533023	SRS18745489	SRP457576	PRJNA1010780	Effect of egr3 knockout on gene expression of dissected zebrafish hearts	GSE241935	Transcriptome Analysis	To screen for Egr3 targets mediating cardiac valve development we assessed gene expression on dissected hearts of egr3 mutants and wild type siblings. Overall design: To evaluate the transcriptional differences underlying the egr3 mutant phenotype we conducted a bulk RNA seq analysis in dissected zebrafish hearts at 48 hpf. We dissected 20 hearts for each biological duplicate of egr3 mutant and wild type sibling samples in cold DMEM with 10% FBS. Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12µl of RNase free water. Analysis of the obtained reads confirmed the 11bp deletion in the mutant samples. 1. Boezio G. L. M. et al. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 16 2023. https://doi.org:10.1242/dmm.049571		pubmed:38748804		egr3 wild type siblings 1	GSM7745908		source name:Heart\|tissue:Heart\|genotype:bns577+/+\|geo loc name:missing\|collection date:missing	egr3 wild type siblings 1	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 2.27.1 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.30.1 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2 and batch corrected using CountClust each biological replicate = one batch Dey K et al. Visualizing the structure of RNA seq expression data using grade of membership models. Genes were classified as significantly differentially expressed at average count > 5 multiple testing adjusted p value < 0.05 and 0.585 < log2FC > 0.585. Assembly: danRer11 Supplementary files format and content: libryr size notmalize amd batch corrected counts	Heart		Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.		tissue:Heart\|genotype:bns577+/+	GSM7745908	GSM7745908: egr3 wild type siblings 1; Danio rerio; RNA Seq	GSM7745908 r1	GSM7745908	1	Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP457576		loader:fastq load.py	E22_3626_Lib_Agatha_egr3_WT1_R1.fastq.gz	fastq	3909248616.0	55045571.0	GSM7745908 r1	0:71.02	A:1048107387;C:905014546;G:907455489;T:1048528690;N:142504	71				1048107387	905014546	907455489	1048528690	142504	SRX21533023	SRS18745489	SRA1702458	MPI for heart and lung research	MPI for heart and lung research	1	0.94958	0.06298	0.74819	0.45762	72	B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2023-08-30	Undetermined	Undetermined	Heart	Cardiovascular System
25322	25322	SRR25810880	SRX21533022	SRS18745488	SRP457576	PRJNA1010780	Effect of egr3 knockout on gene expression of dissected zebrafish hearts	GSE241935	Transcriptome Analysis	To screen for Egr3 targets mediating cardiac valve development we assessed gene expression on dissected hearts of egr3 mutants and wild type siblings. Overall design: To evaluate the transcriptional differences underlying the egr3 mutant phenotype we conducted a bulk RNA seq analysis in dissected zebrafish hearts at 48 hpf. We dissected 20 hearts for each biological duplicate of egr3 mutant and wild type sibling samples in cold DMEM with 10% FBS. Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12µl of RNase free water. Analysis of the obtained reads confirmed the 11bp deletion in the mutant samples. 1. Boezio G. L. M. et al. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 16 2023. https://doi.org:10.1242/dmm.049571		pubmed:38748804		egr3 mutants 2	GSM7745907		source name:Heart\|tissue:Heart\|genotype:bns577 / \|geo loc name:missing\|collection date:missing	egr3 mutants 2	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 2.27.1 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.30.1 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2 and batch corrected using CountClust each biological replicate = one batch Dey K et al. Visualizing the structure of RNA seq expression data using grade of membership models. Genes were classified as significantly differentially expressed at average count > 5 multiple testing adjusted p value < 0.05 and 0.585 < log2FC > 0.585. Assembly: danRer11 Supplementary files format and content: libryr size notmalize amd batch corrected counts	Heart		Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.		tissue:Heart\|genotype:bns577 /	GSM7745907	GSM7745907: egr3 mutants 2; Danio rerio; RNA Seq	GSM7745907 r1	GSM7745907	1	Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP457576		loader:fastq load.py	E22_3626_Lib_Agatha_egr3_Mut2_R1.fastq.gz	fastq	3432675258.0	48483287.0	GSM7745907 r1	0:70.80	A:925832958;C:788551205;G:790129536;T:927993012;N:168547	70				925832958	788551205	790129536	927993012	168547	SRX21533022	SRS18745488	SRA1702458	MPI for heart and lung research	MPI for heart and lung research	1	0.75652	0.04046	0.76455	0.46333	72	B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2023-08-30	Undetermined	Undetermined	Heart	Cardiovascular System
25323	25323	SRR25810881	SRX21533021	SRS18745487	SRP457576	PRJNA1010780	Effect of egr3 knockout on gene expression of dissected zebrafish hearts	GSE241935	Transcriptome Analysis	To screen for Egr3 targets mediating cardiac valve development we assessed gene expression on dissected hearts of egr3 mutants and wild type siblings. Overall design: To evaluate the transcriptional differences underlying the egr3 mutant phenotype we conducted a bulk RNA seq analysis in dissected zebrafish hearts at 48 hpf. We dissected 20 hearts for each biological duplicate of egr3 mutant and wild type sibling samples in cold DMEM with 10% FBS. Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12µl of RNase free water. Analysis of the obtained reads confirmed the 11bp deletion in the mutant samples. 1. Boezio G. L. M. et al. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 16 2023. https://doi.org:10.1242/dmm.049571		pubmed:38748804		egr3 mutants 1	GSM7745906		source name:Heart\|tissue:Heart\|genotype:bns577 / \|geo loc name:missing\|collection date:missing	egr3 mutants 1	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 2.27.1 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.30.1 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2 and batch corrected using CountClust each biological replicate = one batch Dey K et al. Visualizing the structure of RNA seq expression data using grade of membership models. Genes were classified as significantly differentially expressed at average count > 5 multiple testing adjusted p value < 0.05 and 0.585 < log2FC > 0.585. Assembly: danRer11 Supplementary files format and content: libryr size notmalize amd batch corrected counts	Heart		Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.		tissue:Heart\|genotype:bns577 /	GSM7745906	GSM7745906: egr3 mutants 1; Danio rerio; RNA Seq	GSM7745906 r1	GSM7745906	1	Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084 followed by on column DNase digestion DNase Free DNase Set Qiagen 79254 and final elution was performed in 12μl of RNase free water 10ng total RNA was used for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP457576		loader:fastq load.py	E22_3626_Lib_Agatha_egr3_Mut1_R1.fastq.gz	fastq	3838969347.0	54545950.0	GSM7745906 r1	0:70.38	A:1016913415;C:902500250;G:903033204;T:1016194618;N:327860	70				1016913415	902500250	903033204	1016194618	327860	SRX21533021	SRS18745487	SRA1702458	MPI for heart and lung research	MPI for heart and lung research	1	0.9511	0.05017	0.75341	0.47152	72	B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2023-08-30	Undetermined	Undetermined	Heart	Cardiovascular System
29086	29086	SRR27015250	SRX22707800	SRS19700101	SRP475323	PRJNA1047551	Identification of genes important during atrial myocardial morphogenesis	GSE249149	Transcriptome Analysis	Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures. We aimed to identify the genes involved during this process and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.		pubmed:39289341		Wild type zebrafish atrial cardiomyocytes 72 hpf rep 3	GSM7927521		source name:embryonic heart\|tissue:embryonic heart\|cell type:cardiomyocyte\|genotype:wild type\|treatment:72 hpf loc name:missing\|collection date:missing	Wild type zebrafish atrial cardiomyocytes 72 hpf rep 3	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al. Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Assembly: danRer11 Supplementary files format and content: count matrix	embryonic heart		miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		tissue:embryonic heart\|cell type:cardiomyocyte\|genotype:wild type\|treatment:72 hpf	GSM7927521	GSM7927521: Wild type zebrafish atrial cardiomyocytes 72 hpf rep 3; Danio rerio; RNA Seq	GSM7927521 r1	GSM7927521	1	miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP475323		loader:fastq load.py	dst226_zbrf_clt___ACrdmct-age___72h_b03_t01_m01_R1.fastq.gz	fastq	1709509823.0	28403358.0	GSM7927521 r1	0:60.19	A:400293032;C:330429588;G:326652799;T:383291002;N:268843402	60				400293032	330429588	326652799	383291002	268843402	SRX22707800	SRS19700101	SRA1761360	MPI for heart and lung research	MPI for heart and lung research	1	0.90079	0.0827	0.81406	0.64557	35	B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2023-12-01	Larval	Larval	Heart	Cardiovascular System
29087	29087	SRR27015251	SRX22707799	SRS19700100	SRP475323	PRJNA1047551	Identification of genes important during atrial myocardial morphogenesis	GSE249149	Transcriptome Analysis	Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures. We aimed to identify the genes involved during this process and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.		pubmed:39289341		Wild type zebrafish atrial cardiomyocytes 72 hpf rep 2	GSM7927520		source name:embryonic heart\|tissue:embryonic heart\|cell type:cardiomyocyte\|genotype:wild type\|treatment:72 hpf loc name:missing\|collection date:missing	Wild type zebrafish atrial cardiomyocytes 72 hpf rep 2	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al. Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Assembly: danRer11 Supplementary files format and content: count matrix	embryonic heart		miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		tissue:embryonic heart\|cell type:cardiomyocyte\|genotype:wild type\|treatment:72 hpf	GSM7927520	GSM7927520: Wild type zebrafish atrial cardiomyocytes 72 hpf rep 2; Danio rerio; RNA Seq	GSM7927520 r1	GSM7927520	1	miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP475323		loader:fastq load.py	dst226_zbrf_clt___ACrdmct-age___72h_b02_t01_m01_R1.fastq.gz	fastq	1740891025.0	28211981.0	GSM7927520 r1	0:61.71	A:419094150;C:347792831;G:345450108;T:407537501;N:221016435	61				419094150	347792831	345450108	407537501	221016435	SRX22707799	SRS19700100	SRA1761360	MPI for heart and lung research	MPI for heart and lung research	1	0.90091	0.13293	0.78464	0.54281	69	B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2023-12-01	Larval	Larval	Heart	Cardiovascular System
29088	29088	SRR27015252	SRX22707798	SRS19700099	SRP475323	PRJNA1047551	Identification of genes important during atrial myocardial morphogenesis	GSE249149	Transcriptome Analysis	Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures. We aimed to identify the genes involved during this process and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.		pubmed:39289341		Wild type zebrafish atrial cardiomyocytes 72 hpf rep 1	GSM7927519		source name:embryonic heart\|tissue:embryonic heart\|cell type:cardiomyocyte\|genotype:wild type\|treatment:72 hpf loc name:missing\|collection date:missing	Wild type zebrafish atrial cardiomyocytes 72 hpf rep 1	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al. Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Assembly: danRer11 Supplementary files format and content: count matrix	embryonic heart		miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		tissue:embryonic heart\|cell type:cardiomyocyte\|genotype:wild type\|treatment:72 hpf	GSM7927519	GSM7927519: Wild type zebrafish atrial cardiomyocytes 72 hpf rep 1; Danio rerio; RNA Seq	GSM7927519 r1	GSM7927519	1	miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP475323		loader:fastq load.py	dst226_zbrf_clt___ACrdmct-age___72h_b01_t01_m01_R1.fastq.gz	fastq	1930552948.0	30996774.0	GSM7927519 r1	0:62.28	A:468769814;C:389869994;G:387622687;T:454801262;N:229489191	62				468769814	389869994	387622687	454801262	229489191	SRX22707798	SRS19700099	SRA1761360	MPI for heart and lung research	MPI for heart and lung research	1	0.90465	0.10656	0.79586	0.55674	72	B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2023-12-01	Larval	Larval	Heart	Cardiovascular System
29089	29089	SRR27015253	SRX22707797	SRS19700098	SRP475323	PRJNA1047551	Identification of genes important during atrial myocardial morphogenesis	GSE249149	Transcriptome Analysis	Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures. We aimed to identify the genes involved during this process and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.		pubmed:39289341		Wild type zebrafish atrial cardiomyocytes 48 hpf rep 3	GSM7927518		source name:embryonic heart\|tissue:embryonic heart\|cell type:cardiomyocyte\|genotype:wild type\|treatment:48 hpf loc name:missing\|collection date:missing	Wild type zebrafish atrial cardiomyocytes 48 hpf rep 3	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al. Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Assembly: danRer11 Supplementary files format and content: count matrix	embryonic heart		miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		tissue:embryonic heart\|cell type:cardiomyocyte\|genotype:wild type\|treatment:48 hpf	GSM7927518	GSM7927518: Wild type zebrafish atrial cardiomyocytes 48 hpf rep 3; Danio rerio; RNA Seq	GSM7927518 r1	GSM7927518	1	miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP475323		loader:fastq load.py	dst226_zbrf_clt___ACrdmct-age___48h_b03_t01_m01_R1.fastq.gz	fastq	2161847345.0	35921817.0	GSM7927518 r1	0:60.18	A:505467877;C:418329045;G:416403136;T:483063599;N:338583688	60				505467877	418329045	416403136	483063599	338583688	SRX22707797	SRS19700098	SRA1761360	MPI for heart and lung research	MPI for heart and lung research	1	0.89532	0.08355	0.82012	0.68413	35	B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2023-12-01	Hatching	Embryo	Heart	Cardiovascular System
29090	29090	SRR27015254	SRX22707796	SRS19700097	SRP475323	PRJNA1047551	Identification of genes important during atrial myocardial morphogenesis	GSE249149	Transcriptome Analysis	Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures. We aimed to identify the genes involved during this process and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.		pubmed:39289341		Wild type zebrafish atrial cardiomyocytes 48 hpf rep 2	GSM7927517		source name:embryonic heart\|tissue:embryonic heart\|cell type:cardiomyocyte\|genotype:wild type\|treatment:48 hpf loc name:missing\|collection date:missing	Wild type zebrafish atrial cardiomyocytes 48 hpf rep 2	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al. Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Assembly: danRer11 Supplementary files format and content: count matrix	embryonic heart		miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		tissue:embryonic heart\|cell type:cardiomyocyte\|genotype:wild type\|treatment:48 hpf	GSM7927517	GSM7927517: Wild type zebrafish atrial cardiomyocytes 48 hpf rep 2; Danio rerio; RNA Seq	GSM7927517 r1	GSM7927517	1	miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP475323		loader:fastq load.py	dst226_zbrf_clt___ACrdmct-age___48h_b02_t01_m01_R1.fastq.gz	fastq	2065547064.0	31863833.0	GSM7927517 r1	0:64.82	A:530497695;C:434164388;G:434118538;T:518043928;N:148722515	64				530497695	434164388	434118538	518043928	148722515	SRX22707796	SRS19700097	SRA1761360	MPI for heart and lung research	MPI for heart and lung research	1	0.91772	0.17863	0.76828	0.49567	72	B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2023-12-01	Hatching	Embryo	Heart	Cardiovascular System
29091	29091	SRR27015255	SRX22707795	SRS19700096	SRP475323	PRJNA1047551	Identification of genes important during atrial myocardial morphogenesis	GSE249149	Transcriptome Analysis	Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures. We aimed to identify the genes involved during this process and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.		pubmed:39289341		Wild type zebrafish atrial cardiomyocytes 48 hpf rep 1	GSM7927516		source name:embryonic heart\|tissue:embryonic heart\|cell type:cardiomyocyte\|genotype:wild type\|treatment:48 hpf loc name:missing\|collection date:missing	Wild type zebrafish atrial cardiomyocytes 48 hpf rep 1	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al. Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Assembly: danRer11 Supplementary files format and content: count matrix	embryonic heart		miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		tissue:embryonic heart\|cell type:cardiomyocyte\|genotype:wild type\|treatment:48 hpf	GSM7927516	GSM7927516: Wild type zebrafish atrial cardiomyocytes 48 hpf rep 1; Danio rerio; RNA Seq	GSM7927516 r1	GSM7927516	1	miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP475323		loader:fastq load.py	dst226_zbrf_clt___ACrdmct-age___48h_b01_t01_m01_R1.fastq.gz	fastq	1619268089.0	24941754.0	GSM7927516 r1	0:64.92	A:410578311;C:344485123;G:343852178;T:401558739;N:118793738	64				410578311	344485123	343852178	401558739	118793738	SRX22707795	SRS19700096	SRA1761360	MPI for heart and lung research	MPI for heart and lung research	1	0.91693	0.13175	0.77082	0.47511	72	B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2023-12-01	Hatching	Embryo	Heart	Cardiovascular System
29569	29569	SRR27368685	SRX23045203	SRS20006222	SRP480346	PRJNA1057908	An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]	GSE252151	Transcriptome Analysis	cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types predominantly cardiomyocytes. Therefore cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development as they share a number of physiological features with the human heart during development. Therefore we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes validating these genomic regions as cardiac regulatory elements. We share this comprehensive reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells n=3 biological replicates and GFP negative cells 500 000 cells n=3 biological replicates were collected and RNA sequencing was performed on these samples.	parent bioproject:PRJNA1057890			500kGFPneg6 Non cardiomyocytes	GSM7995233		source name:Heart\|tissue:Heart\|cell line:Primary cells\|cell type:Non cardiomyocytes\|genotype:Tgmyl7::GFP\|gfp status:GFPneg\|treatment:Control\|geo loc name:missing\|collection date:missing	500kGFPneg6 Non cardiomyocytes	FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin 2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al 2018 using default parameters. There were two sets of counts obtained the first were the reads mapped to genome Zv9 and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9 Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample	Heart		RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:Heart\|cell line:Primary cells\|cell type:Non cardiomyocytes\|genotype:Tgmyl7::GFP\|gfp status:GFPneg\|treatment:Control	GSM7995233	GSM7995233: 500kGFPneg6 Non cardiomyocytes; Danio rerio; RNA Seq	GSM7995233 r1	GSM7995233	1	RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP480346			500kGFPneg6_S42_L008_R1_001.fastq.gz	fastq	527477356.0	10449387.0	GSM7995233 r1	0:50.48	A:141759410;C:113279303;G:116384028;T:155860577;N:194038	50				141759410	113279303	116384028	155860577	194038	SRX23045203	SRS20006222	SRA1776396	Australian Regenerative Medicine Institute, Monash University	Australian Regenerative Medicine Institute, Monash University	1	0.79175	0.2711	0.7587	0.61924	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-12-27	Undetermined	Larval	Heart	Cardiovascular System
29570	29570	SRR27368686	SRX23045202	SRS20006221	SRP480346	PRJNA1057908	An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]	GSE252151	Transcriptome Analysis	cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types predominantly cardiomyocytes. Therefore cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development as they share a number of physiological features with the human heart during development. Therefore we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes validating these genomic regions as cardiac regulatory elements. We share this comprehensive reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells n=3 biological replicates and GFP negative cells 500 000 cells n=3 biological replicates were collected and RNA sequencing was performed on these samples.	parent bioproject:PRJNA1057890			500kGFPneg5 Non cardiomyocytes	GSM7995232		source name:Heart\|tissue:Heart\|cell line:Primary cells\|cell type:Non cardiomyocytes\|genotype:Tgmyl7::GFP\|gfp status:GFPneg\|treatment:Control\|geo loc name:missing\|collection date:missing	500kGFPneg5 Non cardiomyocytes	FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin 2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al 2018 using default parameters. There were two sets of counts obtained the first were the reads mapped to genome Zv9 and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9 Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample	Heart		RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:Heart\|cell line:Primary cells\|cell type:Non cardiomyocytes\|genotype:Tgmyl7::GFP\|gfp status:GFPneg\|treatment:Control	GSM7995232	GSM7995232: 500kGFPneg5 Non cardiomyocytes; Danio rerio; RNA Seq	GSM7995232 r1	GSM7995232	1	RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP480346			500kGFPneg5_S41_L008_R1_001.fastq.gz	fastq	3356204764.0	66511806.0	GSM7995232 r1	0:50.46	A:860342578;C:766593257;G:774473426;T:953992775;N:802728	50				860342578	766593257	774473426	953992775	802728	SRX23045202	SRS20006221	SRA1776396	Australian Regenerative Medicine Institute, Monash University	Australian Regenerative Medicine Institute, Monash University	1	0.70469	0.23332	0.76992	0.62712	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-12-27	Undetermined	Larval	Heart	Cardiovascular System
29571	29571	SRR27368687	SRX23045201	SRS20006220	SRP480346	PRJNA1057908	An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]	GSE252151	Transcriptome Analysis	cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types predominantly cardiomyocytes. Therefore cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development as they share a number of physiological features with the human heart during development. Therefore we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes validating these genomic regions as cardiac regulatory elements. We share this comprehensive reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells n=3 biological replicates and GFP negative cells 500 000 cells n=3 biological replicates were collected and RNA sequencing was performed on these samples.	parent bioproject:PRJNA1057890			500kGFPneg4 Non cardiomyocytes	GSM7995231		source name:Heart\|tissue:Heart\|cell line:Primary cells\|cell type:Non cardiomyocytes\|genotype:Tgmyl7::GFP\|gfp status:GFPneg\|treatment:Control\|geo loc name:missing\|collection date:missing	500kGFPneg4 Non cardiomyocytes	FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin 2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al 2018 using default parameters. There were two sets of counts obtained the first were the reads mapped to genome Zv9 and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9 Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample	Heart		RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:Heart\|cell line:Primary cells\|cell type:Non cardiomyocytes\|genotype:Tgmyl7::GFP\|gfp status:GFPneg\|treatment:Control	GSM7995231	GSM7995231: 500kGFPneg4 Non cardiomyocytes; Danio rerio; RNA Seq	GSM7995231 r1	GSM7995231	1	RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP480346			500kGFPneg4_S40_L008_R1_001.fastq.gz	fastq	3075367681.0	60986692.0	GSM7995231 r1	0:50.43	A:807059039;C:682279458;G:696326840;T:888937765;N:764579	50				807059039	682279458	696326840	888937765	764579	SRX23045201	SRS20006220	SRA1776396	Australian Regenerative Medicine Institute, Monash University	Australian Regenerative Medicine Institute, Monash University	1	0.74255	0.26699	0.76786	0.63053	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-12-27	Undetermined	Larval	Heart	Cardiovascular System
29572	29572	SRR27368688	SRX23045200	SRS20006219	SRP480346	PRJNA1057908	An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]	GSE252151	Transcriptome Analysis	cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types predominantly cardiomyocytes. Therefore cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development as they share a number of physiological features with the human heart during development. Therefore we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes validating these genomic regions as cardiac regulatory elements. We share this comprehensive reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells n=3 biological replicates and GFP negative cells 500 000 cells n=3 biological replicates were collected and RNA sequencing was performed on these samples.	parent bioproject:PRJNA1057890			30kGFPpos3 Cardiomyocytes	GSM7995230		source name:Heart\|tissue:Heart\|cell line:Primary cells\|cell type:Cardiomyocytes\|genotype:Tgmyl7::GFP\|gfp status:GFPpos\|treatment:Control\|geo loc name:missing\|collection date:missing	30kGFPpos3 Cardiomyocytes	FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin 2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al 2018 using default parameters. There were two sets of counts obtained the first were the reads mapped to genome Zv9 and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9 Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample	Heart		RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:Heart\|cell line:Primary cells\|cell type:Cardiomyocytes\|genotype:Tgmyl7::GFP\|gfp status:GFPpos\|treatment:Control	GSM7995230	GSM7995230: 30kGFPpos3 Cardiomyocytes; Danio rerio; RNA Seq	GSM7995230 r1	GSM7995230	1	RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP480346			30kGFPpos3_S39_L008_R1_001.fastq.gz	fastq	2938808771.0	58361915.0	GSM7995230 r1	0:50.35	A:533261626;C:883704329;G:825929620;T:694986734;N:926462	50				533261626	883704329	825929620	694986734	926462	SRX23045200	SRS20006219	SRA1776396	Australian Regenerative Medicine Institute, Monash University	Australian Regenerative Medicine Institute, Monash University	1	0.12924	0.05415	0.92034	0.70896	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-12-27	Undetermined	Larval	Heart	Cardiovascular System
29573	29573	SRR27368689	SRX23045199	SRS20006218	SRP480346	PRJNA1057908	An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]	GSE252151	Transcriptome Analysis	cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types predominantly cardiomyocytes. Therefore cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development as they share a number of physiological features with the human heart during development. Therefore we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes validating these genomic regions as cardiac regulatory elements. We share this comprehensive reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells n=3 biological replicates and GFP negative cells 500 000 cells n=3 biological replicates were collected and RNA sequencing was performed on these samples.	parent bioproject:PRJNA1057890			30kGFPpos2 Cardiomyocytes	GSM7995229		source name:Heart\|tissue:Heart\|cell line:Primary cells\|cell type:Cardiomyocytes\|genotype:Tgmyl7::GFP\|gfp status:GFPpos\|treatment:Control\|geo loc name:missing\|collection date:missing	30kGFPpos2 Cardiomyocytes	FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin 2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al 2018 using default parameters. There were two sets of counts obtained the first were the reads mapped to genome Zv9 and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9 Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample	Heart		RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:Heart\|cell line:Primary cells\|cell type:Cardiomyocytes\|genotype:Tgmyl7::GFP\|gfp status:GFPpos\|treatment:Control	GSM7995229	GSM7995229: 30kGFPpos2 Cardiomyocytes; Danio rerio; RNA Seq	GSM7995229 r1	GSM7995229	1	RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP480346			30kGFPpos2_S38_L008_R1_001.fastq.gz	fastq	3006409096.0	59645543.0	GSM7995229 r1	0:50.40	A:560839480;C:885691877;G:830121593;T:728932219;N:823927	50				560839480	885691877	830121593	728932219	823927	SRX23045199	SRS20006218	SRA1776396	Australian Regenerative Medicine Institute, Monash University	Australian Regenerative Medicine Institute, Monash University	1	0.17805	0.06115	0.89769	0.68731	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-12-27	Undetermined	Larval	Heart	Cardiovascular System
29574	29574	SRR27368690	SRX23045198	SRS20006217	SRP480346	PRJNA1057908	An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]	GSE252151	Transcriptome Analysis	cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types predominantly cardiomyocytes. Therefore cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development as they share a number of physiological features with the human heart during development. Therefore we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes validating these genomic regions as cardiac regulatory elements. We share this comprehensive reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells n=3 biological replicates and GFP negative cells 500 000 cells n=3 biological replicates were collected and RNA sequencing was performed on these samples.	parent bioproject:PRJNA1057890			30kGFPpos1 Cardiomyocytes	GSM7995228		source name:Heart\|tissue:Heart\|cell line:Primary cells\|cell type:Cardiomyocytes\|genotype:Tgmyl7::GFP\|gfp status:GFPpos\|treatment:Control\|geo loc name:missing\|collection date:missing	30kGFPpos1 Cardiomyocytes	FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin 2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al 2018 using default parameters. There were two sets of counts obtained the first were the reads mapped to genome Zv9 and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9 Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample	Heart		RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:Heart\|cell line:Primary cells\|cell type:Cardiomyocytes\|genotype:Tgmyl7::GFP\|gfp status:GFPpos\|treatment:Control	GSM7995228	GSM7995228: 30kGFPpos1 Cardiomyocytes; Danio rerio; RNA Seq	GSM7995228 r1	GSM7995228	1	RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP480346			30kGFPpos1_S37_L008_R1_001.fastq.gz	fastq	3254639839.0	64665631.0	GSM7995228 r1	0:50.33	A:545193535;C:1023804678;G:938318027;T:746302007;N:1021592	50				545193535	1023804678	938318027	746302007	1021592	SRX23045198	SRS20006217	SRA1776396	Australian Regenerative Medicine Institute, Monash University	Australian Regenerative Medicine Institute, Monash University	1	0.05453	0.01921	0.9643	0.78064	49	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-12-27	Undetermined	Larval	Heart	Cardiovascular System
30006	30006	SRR27663958	SRX23331822	SRS20194274	SRP484810	PRJNA1066877	p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation	GSE253758	Transcriptome Analysis	While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia lymphoma anemia and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics. Particularly our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65 the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary our results uncover the functional role of pro inflammatory signaling during HSPC specification revealed their oscillatory dynamics and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification NFKB+ or NFKB endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.		pubmed:39242546		NFKB biol rep 3	GSM8027552		tissue:endothelial cells\|cell type:endothelial cells\|genotype:NFKB:d2eGFP x kdrl:mCherry\|treatment:kdrl+/NFKB sorted\|geo loc name:missing\|collection date:missing	NFKB biol rep 3	Data was analyzed by ROSALIND® https://rosalind.bio/ with a HyperScale architecture developed by ROSALIND Inc. San Diego CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change p values adjusted p values and normalized abundance values per sample for each gene	endothelial cells	22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope dechorionated with pronase Millipore Sigma; 11459643001 anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer.	RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.	Zebrafish Danio rerio embryos and adults were mated staged raised and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle.	cell type:endothelial cells\|genotype:NFKB:d2eGFP x kdrl:mCherry\|treatment:kdrl+/NFKB sorted	GSM8027552	GSM8027552: NFKB biol rep 3; Danio rerio; RNA Seq	GSM8027552 r1	GSM8027552	1	RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484810		loader:fastq load.py	6-RNA-1001_S6_L001_R1_001.fastq.gz	fastq	7566894200.0	75668942.0	GSM8027552 r1	0:100	A:2055514007;C:1776454819;G:1779667416;T:1955100553;N:157405	100				2055514007	1776454819	1779667416	1955100553	157405	SRX23331822	SRS20194274	SRA1788753	Iowa State University	Iowa State University							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-01-19	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
30007	30007	SRR27663959	SRX23331821	SRS20194275	SRP484810	PRJNA1066877	p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation	GSE253758	Transcriptome Analysis	While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia lymphoma anemia and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics. Particularly our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65 the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary our results uncover the functional role of pro inflammatory signaling during HSPC specification revealed their oscillatory dynamics and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification NFKB+ or NFKB endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.		pubmed:39242546		NFKB biol rep 2	GSM8027551		tissue:endothelial cells\|cell type:endothelial cells\|genotype:NFKB:d2eGFP x kdrl:mCherry\|treatment:kdrl+/NFKB sorted\|geo loc name:missing\|collection date:missing	NFKB biol rep 2	Data was analyzed by ROSALIND® https://rosalind.bio/ with a HyperScale architecture developed by ROSALIND Inc. San Diego CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change p values adjusted p values and normalized abundance values per sample for each gene	endothelial cells	22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope dechorionated with pronase Millipore Sigma; 11459643001 anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer.	RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.	Zebrafish Danio rerio embryos and adults were mated staged raised and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle.	cell type:endothelial cells\|genotype:NFKB:d2eGFP x kdrl:mCherry\|treatment:kdrl+/NFKB sorted	GSM8027551	GSM8027551: NFKB biol rep 2; Danio rerio; RNA Seq	GSM8027551 r1	GSM8027551	1	RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484810		loader:fastq load.py	5-RNA-0901_S5_L001_R1_001.fastq.gz	fastq	8077393600.0	80773936.0	GSM8027551 r1	0:100	A:2195547260;C:1863472493;G:1887149224;T:2131055526;N:169097	100				2195547260	1863472493	1887149224	2131055526	169097	SRX23331821	SRS20194275	SRA1788753	Iowa State University	Iowa State University							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-01-19	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
30008	30008	SRR27663960	SRX23331820	SRS20194273	SRP484810	PRJNA1066877	p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation	GSE253758	Transcriptome Analysis	While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia lymphoma anemia and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics. Particularly our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65 the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary our results uncover the functional role of pro inflammatory signaling during HSPC specification revealed their oscillatory dynamics and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification NFKB+ or NFKB endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.		pubmed:39242546		NFKB biol rep 1	GSM8027550		tissue:endothelial cells\|cell type:endothelial cells\|genotype:NFKB:d2eGFP x kdrl:mCherry\|treatment:kdrl+/NFKB sorted\|geo loc name:missing\|collection date:missing	NFKB biol rep 1	Data was analyzed by ROSALIND® https://rosalind.bio/ with a HyperScale architecture developed by ROSALIND Inc. San Diego CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change p values adjusted p values and normalized abundance values per sample for each gene	endothelial cells	22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope dechorionated with pronase Millipore Sigma; 11459643001 anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer.	RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.	Zebrafish Danio rerio embryos and adults were mated staged raised and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle.	cell type:endothelial cells\|genotype:NFKB:d2eGFP x kdrl:mCherry\|treatment:kdrl+/NFKB sorted	GSM8027550	GSM8027550: NFKB biol rep 1; Danio rerio; RNA Seq	GSM8027550 r1	GSM8027550	1	RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484810		loader:fastq load.py	4-RNA-1001_S4_L001_R1_001.fastq.gz	fastq	6536957300.0	65369573.0	GSM8027550 r1	0:100	A:1764502914;C:1531091007;G:1533764634;T:1707464708;N:134037	100				1764502914	1531091007	1533764634	1707464708	134037	SRX23331820	SRS20194273	SRA1788753	Iowa State University	Iowa State University							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-01-19	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
30009	30009	SRR27663961	SRX23331819	SRS20194272	SRP484810	PRJNA1066877	p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation	GSE253758	Transcriptome Analysis	While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia lymphoma anemia and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics. Particularly our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65 the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary our results uncover the functional role of pro inflammatory signaling during HSPC specification revealed their oscillatory dynamics and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification NFKB+ or NFKB endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.		pubmed:39242546		NFKB+ biol rep 3	GSM8027549		tissue:endothelial cells\|cell type:endothelial cells\|genotype:NFKB:d2eGFP x kdrl:mCherry\|treatment:kdrl+/NFKB+ sorted\|geo loc name:missing\|collection date:missing	NFKB+ biol rep 3	Data was analyzed by ROSALIND® https://rosalind.bio/ with a HyperScale architecture developed by ROSALIND Inc. San Diego CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change p values adjusted p values and normalized abundance values per sample for each gene	endothelial cells	22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope dechorionated with pronase Millipore Sigma; 11459643001 anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer.	RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.	Zebrafish Danio rerio embryos and adults were mated staged raised and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle.	cell type:endothelial cells\|genotype:NFKB:d2eGFP x kdrl:mCherry\|treatment:kdrl+/NFKB+ sorted	GSM8027549	GSM8027549: NFKB+ biol rep 3; Danio rerio; RNA Seq	GSM8027549 r1	GSM8027549	1	RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484810		loader:fastq load.py	3-RNA-1001_S3_L001_R1_001.fastq.gz	fastq	10375249700.0	103752497.0	GSM8027549 r1	0:100	A:2873369145;C:2335823279;G:2356855554;T:2808985435;N:216287	100				2873369145	2335823279	2356855554	2808985435	216287	SRX23331819	SRS20194272	SRA1788753	Iowa State University	Iowa State University							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-01-19	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
30010	30010	SRR27663962	SRX23331818	SRS20194271	SRP484810	PRJNA1066877	p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation	GSE253758	Transcriptome Analysis	While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia lymphoma anemia and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics. Particularly our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65 the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary our results uncover the functional role of pro inflammatory signaling during HSPC specification revealed their oscillatory dynamics and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification NFKB+ or NFKB endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.		pubmed:39242546		NFKB+ biol rep 2	GSM8027548		tissue:endothelial cells\|cell type:endothelial cells\|genotype:NFKB:d2eGFP x kdrl:mCherry\|treatment:kdrl+/NFKB+ sorted\|geo loc name:missing\|collection date:missing	NFKB+ biol rep 2	Data was analyzed by ROSALIND® https://rosalind.bio/ with a HyperScale architecture developed by ROSALIND Inc. San Diego CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change p values adjusted p values and normalized abundance values per sample for each gene	endothelial cells	22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope dechorionated with pronase Millipore Sigma; 11459643001 anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer.	RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.	Zebrafish Danio rerio embryos and adults were mated staged raised and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle.	cell type:endothelial cells\|genotype:NFKB:d2eGFP x kdrl:mCherry\|treatment:kdrl+/NFKB+ sorted	GSM8027548	GSM8027548: NFKB+ biol rep 2; Danio rerio; RNA Seq	GSM8027548 r1	GSM8027548	1	RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484810		loader:fastq load.py	2-RNA-1001_S2_L001_R1_001.fastq.gz	fastq	5743794100.0	57437941.0	GSM8027548 r1	0:100	A:1588561398;C:1297479370;G:1310669617;T:1546965673;N:118042	100				1588561398	1297479370	1310669617	1546965673	118042	SRX23331818	SRS20194271	SRA1788753	Iowa State University	Iowa State University							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-01-19	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
30011	30011	SRR27663963	SRX23331817	SRS20194270	SRP484810	PRJNA1066877	p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation	GSE253758	Transcriptome Analysis	While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia lymphoma anemia and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics. Particularly our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65 the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary our results uncover the functional role of pro inflammatory signaling during HSPC specification revealed their oscillatory dynamics and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification NFKB+ or NFKB endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.		pubmed:39242546		NFKB+ biol rep 1	GSM8027547		tissue:endothelial cells\|cell type:endothelial cells\|genotype:NFKB:d2eGFP x kdrl:mCherry\|treatment:kdrl+/NFKB+ sorted\|geo loc name:missing\|collection date:missing	NFKB+ biol rep 1	Data was analyzed by ROSALIND® https://rosalind.bio/ with a HyperScale architecture developed by ROSALIND Inc. San Diego CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change p values adjusted p values and normalized abundance values per sample for each gene	endothelial cells	22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope dechorionated with pronase Millipore Sigma; 11459643001 anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer.	RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.	Zebrafish Danio rerio embryos and adults were mated staged raised and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle.	cell type:endothelial cells\|genotype:NFKB:d2eGFP x kdrl:mCherry\|treatment:kdrl+/NFKB+ sorted	GSM8027547	GSM8027547: NFKB+ biol rep 1; Danio rerio; RNA Seq	GSM8027547 r1	GSM8027547	1	RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP484810		loader:fastq load.py	1-RNA-0917_S1_L001_R1_001.fastq.gz	fastq	6201542500.0	62015425.0	GSM8027547 r1	0:100	A:1696049302;C:1431941155;G:1441395671;T:1632027072;N:129300	100				1696049302	1431941155	1441395671	1632027072	129300	SRX23331817	SRS20194270	SRA1788753	Iowa State University	Iowa State University							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2024-01-19	Multi-stage	Multi-stage	Endothelium	Cardiovascular System
30512	30512	SRR27764782	SRX23429747	SRS20284188	SRP486526	PRJNA1070616	Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response	GSE254466	Transcriptome Analysis	The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l also known as Scaf1 promotes CIII CIV super assembly and energetic efficiency in zebrafish mice and humans. Here we studied the role of a second member of the Cox7a family Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism. Already in homeostatic conditions cox7a1 / hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical revealing that there is a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 / mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq. 4 pools each comprising 5 ventricles were sequenced per condition.		pubmed:38701784		Cardiac ventricle cox7a1 / replicate 4	GSM8042779		source name:Cardiac Ventricle\|tissue:Cardiac Ventricle\|genotype:Cox7a mut\|treatment:7days post cryoinjury\|geo loc name:missing\|collection date:missing	Cardiac ventricle cox7a1 / replicate 4	Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts tab seprated values	Cardiac Ventricle		4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol		tissue:Cardiac Ventricle\|genotype:Cox7a mut\|treatment:7days post cryoinjury	GSM8042779	GSM8042779: Cardiac ventricle cox7a1 / replicate 4; Danio rerio; RNA Seq	GSM8042779 r1	GSM8042779	1	4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP486526			KO_10_Directional_S8_R1_001.fastq.gz	fastq	8619450300.0	86194503.0	GSM8042779 r1	0:100	A:2183264320;C:2042597849;G:2002385828;T:2389908983;N:1293320	100				2183264320	2042597849	2002385828	2389908983	1293320	SRX23429747	SRS20284188	SRA1793874	University of Bern	University of Bern							B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	Switzerland	2024-01-29	Undetermined	Adult	Heart	Cardiovascular System
30513	30513	SRR27764783	SRX23429746	SRS20284187	SRP486526	PRJNA1070616	Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response	GSE254466	Transcriptome Analysis	The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l also known as Scaf1 promotes CIII CIV super assembly and energetic efficiency in zebrafish mice and humans. Here we studied the role of a second member of the Cox7a family Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism. Already in homeostatic conditions cox7a1 / hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical revealing that there is a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 / mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq. 4 pools each comprising 5 ventricles were sequenced per condition.		pubmed:38701784		Cardiac ventricle cox7a1 / replicate 3	GSM8042778		source name:Cardiac Ventricle\|tissue:Cardiac Ventricle\|genotype:Cox7a mut\|treatment:7days post cryoinjury\|geo loc name:missing\|collection date:missing	Cardiac ventricle cox7a1 / replicate 3	Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts tab seprated values	Cardiac Ventricle		4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol		tissue:Cardiac Ventricle\|genotype:Cox7a mut\|treatment:7days post cryoinjury	GSM8042778	GSM8042778: Cardiac ventricle cox7a1 / replicate 3; Danio rerio; RNA Seq	GSM8042778 r1	GSM8042778	1	4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP486526			KO_9_Directional_S7_R1_001.fastq.gz	fastq	6466746100.0	64667461.0	GSM8042778 r1	0:100	A:1708351950;C:1464168743;G:1452219209;T:1841033764;N:972434	100				1708351950	1464168743	1452219209	1841033764	972434	SRX23429746	SRS20284187	SRA1793874	University of Bern	University of Bern							B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	Switzerland	2024-01-29	Undetermined	Adult	Heart	Cardiovascular System
30514	30514	SRR27764784	SRX23429745	SRS20284186	SRP486526	PRJNA1070616	Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response	GSE254466	Transcriptome Analysis	The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l also known as Scaf1 promotes CIII CIV super assembly and energetic efficiency in zebrafish mice and humans. Here we studied the role of a second member of the Cox7a family Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism. Already in homeostatic conditions cox7a1 / hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical revealing that there is a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 / mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq. 4 pools each comprising 5 ventricles were sequenced per condition.		pubmed:38701784		Cardiac ventricle cox7a1 / replicate 2	GSM8042777		source name:Cardiac Ventricle\|tissue:Cardiac Ventricle\|genotype:Cox7a mut\|treatment:7days post cryoinjury\|geo loc name:missing\|collection date:missing	Cardiac ventricle cox7a1 / replicate 2	Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts tab seprated values	Cardiac Ventricle		4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol		tissue:Cardiac Ventricle\|genotype:Cox7a mut\|treatment:7days post cryoinjury	GSM8042777	GSM8042777: Cardiac ventricle cox7a1 / replicate 2; Danio rerio; RNA Seq	GSM8042777 r1	GSM8042777	1	4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP486526			KO_8_Directional_S6_R1_001.fastq.gz	fastq	6766795300.0	67667953.0	GSM8042777 r1	0:100	A:1803038642;C:1540664299;G:1518741633;T:1903355305;N:995421	100				1803038642	1540664299	1518741633	1903355305	995421	SRX23429745	SRS20284186	SRA1793874	University of Bern	University of Bern							B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	Switzerland	2024-01-29	Undetermined	Adult	Heart	Cardiovascular System
30515	30515	SRR27764785	SRX23429744	SRS20284185	SRP486526	PRJNA1070616	Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response	GSE254466	Transcriptome Analysis	The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l also known as Scaf1 promotes CIII CIV super assembly and energetic efficiency in zebrafish mice and humans. Here we studied the role of a second member of the Cox7a family Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism. Already in homeostatic conditions cox7a1 / hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical revealing that there is a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 / mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq. 4 pools each comprising 5 ventricles were sequenced per condition.		pubmed:38701784		Cardiac ventricle cox7a1 / replicate 1	GSM8042776		source name:Cardiac Ventricle\|tissue:Cardiac Ventricle\|genotype:Cox7a mut\|treatment:7days post cryoinjury\|geo loc name:missing\|collection date:missing	Cardiac ventricle cox7a1 / replicate 1	Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts tab seprated values	Cardiac Ventricle		4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol		tissue:Cardiac Ventricle\|genotype:Cox7a mut\|treatment:7days post cryoinjury	GSM8042776	GSM8042776: Cardiac ventricle cox7a1 / replicate 1; Danio rerio; RNA Seq	GSM8042776 r1	GSM8042776	1	4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP486526			KO_7_Directional_S5_R1_001.fastq.gz	fastq	5583049300.0	55830493.0	GSM8042776 r1	0:100	A:1479820662;C:1265599242;G:1251078421;T:1585727832;N:823143	100				1479820662	1265599242	1251078421	1585727832	823143	SRX23429744	SRS20284185	SRA1793874	University of Bern	University of Bern							B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	Switzerland	2024-01-29	Undetermined	Adult	Heart	Cardiovascular System
30516	30516	SRR27764786	SRX23429743	SRS20284184	SRP486526	PRJNA1070616	Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response	GSE254466	Transcriptome Analysis	The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l also known as Scaf1 promotes CIII CIV super assembly and energetic efficiency in zebrafish mice and humans. Here we studied the role of a second member of the Cox7a family Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism. Already in homeostatic conditions cox7a1 / hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical revealing that there is a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 / mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq. 4 pools each comprising 5 ventricles were sequenced per condition.		pubmed:38701784		Cardiac ventricle wt sibling replicate 4	GSM8042775		source name:Cardiac Ventricle\|tissue:Cardiac Ventricle\|genotype:WT\|treatment:7days post cryoinjury\|geo loc name:missing\|collection date:missing	Cardiac ventricle wt sibling replicate 4	Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts tab seprated values	Cardiac Ventricle		4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol		tissue:Cardiac Ventricle\|genotype:WT\|treatment:7days post cryoinjury	GSM8042775	GSM8042775: Cardiac ventricle wt sibling replicate 4; Danio rerio; RNA Seq	GSM8042775 r1	GSM8042775	1	4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP486526			WT_5_Directional_S4_R1_001.fastq.gz	fastq	6851217800.0	68512178.0	GSM8042775 r1	0:100	A:1837112549;C:1539284911;G:1515596368;T:1958221274;N:1002698	100				1837112549	1539284911	1515596368	1958221274	1002698	SRX23429743	SRS20284184	SRA1793874	University of Bern	University of Bern							B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	Switzerland	2024-01-29	Undetermined	Adult	Heart	Cardiovascular System
30517	30517	SRR27764787	SRX23429742	SRS20284183	SRP486526	PRJNA1070616	Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response	GSE254466	Transcriptome Analysis	The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l also known as Scaf1 promotes CIII CIV super assembly and energetic efficiency in zebrafish mice and humans. Here we studied the role of a second member of the Cox7a family Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism. Already in homeostatic conditions cox7a1 / hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical revealing that there is a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 / mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq. 4 pools each comprising 5 ventricles were sequenced per condition.		pubmed:38701784		Cardiac ventricle wt sibling replicate 3	GSM8042774		source name:Cardiac Ventricle\|tissue:Cardiac Ventricle\|genotype:WT\|treatment:7days post cryoinjury\|geo loc name:missing\|collection date:missing	Cardiac ventricle wt sibling replicate 3	Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts tab seprated values	Cardiac Ventricle		4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol		tissue:Cardiac Ventricle\|genotype:WT\|treatment:7days post cryoinjury	GSM8042774	GSM8042774: Cardiac ventricle wt sibling replicate 3; Danio rerio; RNA Seq	GSM8042774 r1	GSM8042774	1	4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP486526			WT_3_Directional_S3_R1_001.fastq.gz	fastq	7036251700.0	70362517.0	GSM8042774 r1	0:100	A:1881612688;C:1574593657;G:1570342252;T:2008668471;N:1034632	100				1881612688	1574593657	1570342252	2008668471	1034632	SRX23429742	SRS20284183	SRA1793874	University of Bern	University of Bern							B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	Switzerland	2024-01-29	Undetermined	Adult	Heart	Cardiovascular System
30518	30518	SRR27764788	SRX23429741	SRS20284182	SRP486526	PRJNA1070616	Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response	GSE254466	Transcriptome Analysis	The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l also known as Scaf1 promotes CIII CIV super assembly and energetic efficiency in zebrafish mice and humans. Here we studied the role of a second member of the Cox7a family Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism. Already in homeostatic conditions cox7a1 / hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical revealing that there is a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 / mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq. 4 pools each comprising 5 ventricles were sequenced per condition.		pubmed:38701784		Cardiac ventricle wt sibling replicate 2	GSM8042773		source name:Cardiac Ventricle\|tissue:Cardiac Ventricle\|genotype:WT\|treatment:7days post cryoinjury\|geo loc name:missing\|collection date:missing	Cardiac ventricle wt sibling replicate 2	Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts tab seprated values	Cardiac Ventricle		4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol		tissue:Cardiac Ventricle\|genotype:WT\|treatment:7days post cryoinjury	GSM8042773	GSM8042773: Cardiac ventricle wt sibling replicate 2; Danio rerio; RNA Seq	GSM8042773 r1	GSM8042773	1	4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP486526			WT_2_Directional_S2_R1_001.fastq.gz	fastq	6856428200.0	68564282.0	GSM8042773 r1	0:100	A:1790369167;C:1572129686;G:1566120109;T:1926782247;N:1026991	100				1790369167	1572129686	1566120109	1926782247	1026991	SRX23429741	SRS20284182	SRA1793874	University of Bern	University of Bern							B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	Switzerland	2024-01-29	Undetermined	Adult	Heart	Cardiovascular System
30519	30519	SRR27764789	SRX23429740	SRS20284181	SRP486526	PRJNA1070616	Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response	GSE254466	Transcriptome Analysis	The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l also known as Scaf1 promotes CIII CIV super assembly and energetic efficiency in zebrafish mice and humans. Here we studied the role of a second member of the Cox7a family Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism. Already in homeostatic conditions cox7a1 / hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical revealing that there is a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 / mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq. 4 pools each comprising 5 ventricles were sequenced per condition.		pubmed:38701784		Cardiac ventricle wt sibling replicate 1	GSM8042772		source name:Cardiac Ventricle\|tissue:Cardiac Ventricle\|genotype:WT\|treatment:7days post cryoinjury\|geo loc name:missing\|collection date:missing	Cardiac ventricle wt sibling replicate 1	Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts tab seprated values	Cardiac Ventricle		4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol		tissue:Cardiac Ventricle\|genotype:WT\|treatment:7days post cryoinjury	GSM8042772	GSM8042772: Cardiac ventricle wt sibling replicate 1; Danio rerio; RNA Seq	GSM8042772 r1	GSM8042772	1	4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the "NEBNext Ultra II Directional RNA library prep Kit for Illumina" following manufacturer´s protocol		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP486526			WT_1_Directional_S1_R1_001.fastq.gz	fastq	7089416800.0	70894168.0	GSM8042772 r1	0:100	A:1855346146;C:1626812736;G:1599932420;T:2006283874;N:1041624	100				1855346146	1626812736	1599932420	2006283874	1041624	SRX23429740	SRS20284181	SRA1793874	University of Bern	University of Bern							B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	Switzerland	2024-01-29	Undetermined	Adult	Heart	Cardiovascular System
31502	31502	SRR28411462	SRX24015869	SRS20810998	SRP497025	PRJNA1090509	The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139	GSE262169	Transcriptome Analysis	The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration but many questions remain about its exact role. Here we show that MyD88 a key component of the innate immune response controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration. We find in cryoinjured myd88 / ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population. Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 / endocardium and increased myofibroblasts and scarring. Notably endothelial specific overexpression of myd88 reverses these neutrophil fibrotic and scarring phenotypes. Mechanistically we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway and using loss and gain of function tools show that it controls neutrophil recruitment. Altogether these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 / untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing	parent bioproject:PRJNA1090894	pubmed:39271818		injured tissue myd88+/+ 24 hpci 2	GSM8159071		source name:cardiac ventricles\|tissue:cardiac ventricles\|cell type:ventricular cells\|genotype:myd88+/+\|treatment:cardiac cryoinjury\|geo loc name:missing\|collection date:missing	injured tissue myd88+/+ 24 hpci 2	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5 multiple testing adjusted p value < 0.05 and 0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts	cardiac ventricles	untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction	RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture’s protocol Vazyme.		tissue:cardiac ventricles\|cell type:ventricular cells\|genotype:myd88+/+\|treatment:cardiac cryoinjury	GSM8159071	GSM8159071: injured tissue myd88+/+ 24 hpci 2; Danio rerio; RNA Seq	GSM8159071 r1	GSM8159071	1	RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP497025		loader:fastq load.py	Pinelopi_WT2_24h_pci_R1.fastq.gz	fastq	2454645976.0	33159360.0	GSM8159071 r1	0:74.03	A:660213492;C:527347733;G:572126573;T:694765347;N:192831	74				660213492	527347733	572126573	694765347	192831	SRX24015869	SRS20810998	SRA1830778	MPI for heart and lung research	MPI for heart and lung research							B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Germany	2024-03-21	Undetermined	Undetermined	Heart	Cardiovascular System
31503	31503	SRR28411463	SRX24015868	SRS20810997	SRP497025	PRJNA1090509	The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139	GSE262169	Transcriptome Analysis	The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration but many questions remain about its exact role. Here we show that MyD88 a key component of the innate immune response controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration. We find in cryoinjured myd88 / ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population. Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 / endocardium and increased myofibroblasts and scarring. Notably endothelial specific overexpression of myd88 reverses these neutrophil fibrotic and scarring phenotypes. Mechanistically we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway and using loss and gain of function tools show that it controls neutrophil recruitment. Altogether these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 / untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing	parent bioproject:PRJNA1090894	pubmed:39271818		injured tissue myd88+/+ 1 hpci 2	GSM8159070		source name:cardiac ventricles\|tissue:cardiac ventricles\|cell type:ventricular cells\|genotype:myd88+/+\|treatment:cardiac cryoinjury\|geo loc name:missing\|collection date:missing	injured tissue myd88+/+ 1 hpci 2	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5 multiple testing adjusted p value < 0.05 and 0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts	cardiac ventricles	untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction	RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture’s protocol Vazyme.		tissue:cardiac ventricles\|cell type:ventricular cells\|genotype:myd88+/+\|treatment:cardiac cryoinjury	GSM8159070	GSM8159070: injured tissue myd88+/+ 1 hpci 2; Danio rerio; RNA Seq	GSM8159070 r1	GSM8159070	1	RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP497025		loader:fastq load.py	Pinelopi_WT2_1h_pci_R1.fastq.gz	fastq	2674654542.0	36003719.0	GSM8159070 r1	0:74.29	A:713621237;C:556223861;G:630990745;T:773686189;N:132510	74				713621237	556223861	630990745	773686189	132510	SRX24015868	SRS20810997	SRA1830778	MPI for heart and lung research	MPI for heart and lung research							B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Germany	2024-03-21	Undetermined	Undetermined	Heart	Cardiovascular System
31504	31504	SRR28411464	SRX24015867	SRS20810996	SRP497025	PRJNA1090509	The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139	GSE262169	Transcriptome Analysis	The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration but many questions remain about its exact role. Here we show that MyD88 a key component of the innate immune response controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration. We find in cryoinjured myd88 / ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population. Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 / endocardium and increased myofibroblasts and scarring. Notably endothelial specific overexpression of myd88 reverses these neutrophil fibrotic and scarring phenotypes. Mechanistically we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway and using loss and gain of function tools show that it controls neutrophil recruitment. Altogether these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 / untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing	parent bioproject:PRJNA1090894	pubmed:39271818		ventricle myd88+/+ untouched 2	GSM8159069		source name:cardiac ventricles\|tissue:cardiac ventricles\|cell type:ventricular cells\|genotype:myd88+/+\|treatment: \|geo loc name:missing\|collection date:missing	ventricle myd88+/+ untouched 2	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5 multiple testing adjusted p value < 0.05 and 0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts	cardiac ventricles	untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction	RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture’s protocol Vazyme.		tissue:cardiac ventricles\|cell type:ventricular cells\|genotype:myd88+/+\|treatment:	GSM8159069	GSM8159069: ventricle myd88+/+ untouched 2; Danio rerio; RNA Seq	GSM8159069 r1	GSM8159069	1	RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP497025		loader:fastq load.py	Pinelopi_WT2_0h_pci_R1.fastq.gz	fastq	2092632406.0	28163739.0	GSM8159069 r1	0:74.30	A:560190602;C:446185315;G:485011548;T:601082958;N:161983	74				560190602	446185315	485011548	601082958	161983	SRX24015867	SRS20810996	SRA1830778	MPI for heart and lung research	MPI for heart and lung research							B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Germany	2024-03-21	Undetermined	Undetermined	Heart	Cardiovascular System
31505	31505	SRR28411465	SRX24015866	SRS20810995	SRP497025	PRJNA1090509	The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139	GSE262169	Transcriptome Analysis	The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration but many questions remain about its exact role. Here we show that MyD88 a key component of the innate immune response controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration. We find in cryoinjured myd88 / ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population. Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 / endocardium and increased myofibroblasts and scarring. Notably endothelial specific overexpression of myd88 reverses these neutrophil fibrotic and scarring phenotypes. Mechanistically we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway and using loss and gain of function tools show that it controls neutrophil recruitment. Altogether these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 / untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing	parent bioproject:PRJNA1090894	pubmed:39271818		injured tissue myd88+/+ 24 hpci 1	GSM8159068		source name:cardiac ventricles\|tissue:cardiac ventricles\|cell type:ventricular cells\|genotype:myd88+/+\|treatment:cardiac cryoinjury\|geo loc name:missing\|collection date:missing	injured tissue myd88+/+ 24 hpci 1	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5 multiple testing adjusted p value < 0.05 and 0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts	cardiac ventricles	untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction	RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture’s protocol Vazyme.		tissue:cardiac ventricles\|cell type:ventricular cells\|genotype:myd88+/+\|treatment:cardiac cryoinjury	GSM8159068	GSM8159068: injured tissue myd88+/+ 24 hpci 1; Danio rerio; RNA Seq	GSM8159068 r1	GSM8159068	1	RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP497025		loader:fastq load.py	Pinelopi_WT1_24h_pci_R1.fastq.gz	fastq	1060148110.0	14341826.0	GSM8159068 r1	0:73.92	A:290655996;C:222128471;G:247491826;T:299784598;N:87219	73				290655996	222128471	247491826	299784598	87219	SRX24015866	SRS20810995	SRA1830778	MPI for heart and lung research	MPI for heart and lung research							B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Germany	2024-03-21	Undetermined	Undetermined	Heart	Cardiovascular System
31506	31506	SRR28411466	SRX24015865	SRS20810994	SRP497025	PRJNA1090509	The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139	GSE262169	Transcriptome Analysis	The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration but many questions remain about its exact role. Here we show that MyD88 a key component of the innate immune response controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration. We find in cryoinjured myd88 / ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population. Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 / endocardium and increased myofibroblasts and scarring. Notably endothelial specific overexpression of myd88 reverses these neutrophil fibrotic and scarring phenotypes. Mechanistically we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway and using loss and gain of function tools show that it controls neutrophil recruitment. Altogether these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 / untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing	parent bioproject:PRJNA1090894	pubmed:39271818		injured tissue myd88+/+ 1 hpci 1	GSM8159067		source name:cardiac ventricles\|tissue:cardiac ventricles\|cell type:ventricular cells\|genotype:myd88+/+\|treatment:cardiac cryoinjury\|geo loc name:missing\|collection date:missing	injured tissue myd88+/+ 1 hpci 1	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5 multiple testing adjusted p value < 0.05 and 0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts	cardiac ventricles	untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction	RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture’s protocol Vazyme.		tissue:cardiac ventricles\|cell type:ventricular cells\|genotype:myd88+/+\|treatment:cardiac cryoinjury	GSM8159067	GSM8159067: injured tissue myd88+/+ 1 hpci 1; Danio rerio; RNA Seq	GSM8159067 r1	GSM8159067	1	RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP497025		loader:fastq load.py	Pinelopi_WT1_1h_pci_R1.fastq.gz	fastq	2594786024.0	34913792.0	GSM8159067 r1	0:74.32	A:689702458;C:551265040;G:603307580;T:750425733;N:85213	74				689702458	551265040	603307580	750425733	85213	SRX24015865	SRS20810994	SRA1830778	MPI for heart and lung research	MPI for heart and lung research							B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Germany	2024-03-21	Undetermined	Undetermined	Heart	Cardiovascular System
31507	31507	SRR28411467	SRX24015864	SRS20810993	SRP497025	PRJNA1090509	The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139	GSE262169	Transcriptome Analysis	The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration but many questions remain about its exact role. Here we show that MyD88 a key component of the innate immune response controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration. We find in cryoinjured myd88 / ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population. Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 / endocardium and increased myofibroblasts and scarring. Notably endothelial specific overexpression of myd88 reverses these neutrophil fibrotic and scarring phenotypes. Mechanistically we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway and using loss and gain of function tools show that it controls neutrophil recruitment. Altogether these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 / untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing	parent bioproject:PRJNA1090894	pubmed:39271818		ventricle myd88+/+ untouched 1	GSM8159066		source name:cardiac ventricles\|tissue:cardiac ventricles\|cell type:ventricular cells\|genotype:myd88+/+\|treatment: \|geo loc name:missing\|collection date:missing	ventricle myd88+/+ untouched 1	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5 multiple testing adjusted p value < 0.05 and 0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts	cardiac ventricles	untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction	RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture’s protocol Vazyme.		tissue:cardiac ventricles\|cell type:ventricular cells\|genotype:myd88+/+\|treatment:	GSM8159066	GSM8159066: ventricle myd88+/+ untouched 1; Danio rerio; RNA Seq	GSM8159066 r1	GSM8159066	1	RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP497025		loader:fastq load.py	Pinelopi_WT1_0h_pci_R1.fastq.gz	fastq	2123516005.0	28595227.0	GSM8159066 r1	0:74.26	A:562046544;C:458761205;G:496224794;T:606313940;N:169522	74				562046544	458761205	496224794	606313940	169522	SRX24015864	SRS20810993	SRA1830778	MPI for heart and lung research	MPI for heart and lung research							B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Germany	2024-03-21	Undetermined	Undetermined	Heart	Cardiovascular System
31508	31508	SRR28411468	SRX24015863	SRS20810992	SRP497025	PRJNA1090509	The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139	GSE262169	Transcriptome Analysis	The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration but many questions remain about its exact role. Here we show that MyD88 a key component of the innate immune response controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration. We find in cryoinjured myd88 / ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population. Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 / endocardium and increased myofibroblasts and scarring. Notably endothelial specific overexpression of myd88 reverses these neutrophil fibrotic and scarring phenotypes. Mechanistically we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway and using loss and gain of function tools show that it controls neutrophil recruitment. Altogether these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 / untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing	parent bioproject:PRJNA1090894	pubmed:39271818		injured tissue myd88 / 24 hpci 2	GSM8159065		source name:cardiac ventricles\|tissue:cardiac ventricles\|cell type:ventricular cells\|genotype:myd88 / \|treatment:cardiac cryoinjury\|geo loc name:missing\|collection date:missing	injured tissue myd88 / 24 hpci 2	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5 multiple testing adjusted p value < 0.05 and 0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts	cardiac ventricles	untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction	RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture’s protocol Vazyme.		tissue:cardiac ventricles\|cell type:ventricular cells\|genotype:myd88 / \|treatment:cardiac cryoinjury	GSM8159065	GSM8159065: injured tissue myd88 / 24 hpci 2; Danio rerio; RNA Seq	GSM8159065 r1	GSM8159065	1	RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP497025		loader:fastq load.py	Pinelopi_Homo2_24h_pci_R1.fastq.gz	fastq	2509143345.0	33915175.0	GSM8159065 r1	0:73.98	A:669128241;C:547606289;G:587771598;T:704439682;N:197535	73				669128241	547606289	587771598	704439682	197535	SRX24015863	SRS20810992	SRA1830778	MPI for heart and lung research	MPI for heart and lung research							B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Germany	2024-03-21	Undetermined	Undetermined	Heart	Cardiovascular System
31509	31509	SRR28411469	SRX24015862	SRS20810991	SRP497025	PRJNA1090509	The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139	GSE262169	Transcriptome Analysis	The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration but many questions remain about its exact role. Here we show that MyD88 a key component of the innate immune response controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration. We find in cryoinjured myd88 / ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population. Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 / endocardium and increased myofibroblasts and scarring. Notably endothelial specific overexpression of myd88 reverses these neutrophil fibrotic and scarring phenotypes. Mechanistically we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway and using loss and gain of function tools show that it controls neutrophil recruitment. Altogether these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 / untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing	parent bioproject:PRJNA1090894	pubmed:39271818		injured tissue myd88 / 1 hpci 2	GSM8159064		source name:cardiac ventricles\|tissue:cardiac ventricles\|cell type:ventricular cells\|genotype:myd88 / \|treatment:cardiac cryoinjury\|geo loc name:missing\|collection date:missing	injured tissue myd88 / 1 hpci 2	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5 multiple testing adjusted p value < 0.05 and 0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts	cardiac ventricles	untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction	RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture’s protocol Vazyme.		tissue:cardiac ventricles\|cell type:ventricular cells\|genotype:myd88 / \|treatment:cardiac cryoinjury	GSM8159064	GSM8159064: injured tissue myd88 / 1 hpci 2; Danio rerio; RNA Seq	GSM8159064 r1	GSM8159064	1	RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP497025		loader:fastq load.py	Pinelopi_Homo2_1h_pci_R1.fastq.gz	fastq	2584847185.0	34784917.0	GSM8159064 r1	0:74.31	A:690941775;C:542509296;G:605002938;T:746301098;N:92078	74				690941775	542509296	605002938	746301098	92078	SRX24015862	SRS20810991	SRA1830778	MPI for heart and lung research	MPI for heart and lung research							B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Germany	2024-03-21	Undetermined	Undetermined	Heart	Cardiovascular System
31510	31510	SRR28411470	SRX24015861	SRS20810990	SRP497025	PRJNA1090509	The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139	GSE262169	Transcriptome Analysis	The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration but many questions remain about its exact role. Here we show that MyD88 a key component of the innate immune response controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration. We find in cryoinjured myd88 / ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population. Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 / endocardium and increased myofibroblasts and scarring. Notably endothelial specific overexpression of myd88 reverses these neutrophil fibrotic and scarring phenotypes. Mechanistically we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway and using loss and gain of function tools show that it controls neutrophil recruitment. Altogether these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 / untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing	parent bioproject:PRJNA1090894	pubmed:39271818		ventricle myd88 / untouched 2	GSM8159063		source name:cardiac ventricles\|tissue:cardiac ventricles\|cell type:ventricular cells\|genotype:myd88 / \|treatment: \|geo loc name:missing\|collection date:missing	ventricle myd88 / untouched 2	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5 multiple testing adjusted p value < 0.05 and 0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts	cardiac ventricles	untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction	RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture’s protocol Vazyme.		tissue:cardiac ventricles\|cell type:ventricular cells\|genotype:myd88 / \|treatment:	GSM8159063	GSM8159063: ventricle myd88 / untouched 2; Danio rerio; RNA Seq	GSM8159063 r1	GSM8159063	1	RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP497025		loader:fastq load.py	Pinelopi_Homo2_0h_pci_R1.fastq.gz	fastq	2178164776.0	29313471.0	GSM8159063 r1	0:74.31	A:588370831;C:457110464;G:507924919;T:624586577;N:171985	74				588370831	457110464	507924919	624586577	171985	SRX24015861	SRS20810990	SRA1830778	MPI for heart and lung research	MPI for heart and lung research							B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Germany	2024-03-21	Undetermined	Undetermined	Heart	Cardiovascular System
31511	31511	SRR28411471	SRX24015860	SRS20810989	SRP497025	PRJNA1090509	The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst139	GSE262169	Transcriptome Analysis	The innate immune response is triggered xxx post injury and its spatiotemporal dynamics are critical for regeneration but many questions remain about its exact role. Here we show that MyD88 a key component of the innate immune response controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration. We find in cryoinjured myd88 / ventricles a significant reduction in neutrophil and macrophage numbers as well as the expansion of a collagen rich endocardial population. Further analyses reveal compromised PI3K/AKT pathway activation in the myd88 / endocardium and increased myofibroblasts and scarring. Notably endothelial specific overexpression of myd88 reverses these neutrophil fibrotic and scarring phenotypes. Mechanistically we identify the endocardial derived chemokine gene cxcl18b as a target of the MyD88 signaling pathway and using loss and gain of function tools show that it controls neutrophil recruitment. Altogether these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis during tissue regeneration. Overall design: RNA was isolated from myd88+/+ and myd88 / untouched ventricles and cryoinjured tissues at 1 and 24 hours post cryoinjury hpci and analyzed using bulk RNA sequencing	parent bioproject:PRJNA1090894	pubmed:39271818		injured tissue myd88 / 24 hpci 1	GSM8159062		source name:cardiac ventricles\|tissue:cardiac ventricles\|cell type:ventricular cells\|genotype:myd88 / \|treatment:cardiac cryoinjury\|geo loc name:missing\|collection date:missing	injured tissue myd88 / 24 hpci 1	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 99 with STAR 2.7.3a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 2.21.7 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. The raw count matrix was normalized with DESeq2 version 1.26.0 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5 multiple testing adjusted p value < 0.05 and 0.585 < log2FC > 0.585. Gene counts were established with featureCounts 1.6.5 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: DanRer11 Supplementary files format and content: library normilzed counts	cardiac ventricles	untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction	RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture’s protocol Vazyme.		tissue:cardiac ventricles\|cell type:ventricular cells\|genotype:myd88 / \|treatment:cardiac cryoinjury	GSM8159062	GSM8159062: injured tissue myd88 / 24 hpci 1; Danio rerio; RNA Seq	GSM8159062 r1	GSM8159062	1	RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase free DNase set Qiagen to avoid contamination by genomic DNA. 400ng of total RNA was used as input for VAHTS Stranded mRNA seq Library preparation V6 following manufacture's protocol Vazyme.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP497025		loader:fastq load.py	Pinelopi_Homo1_24h_pci_R1.fastq.gz	fastq	2323298254.0	31332951.0	GSM8159062 r1	0:74.15	A:621931320;C:501998000;G:541224122;T:657957821;N:186991	74				621931320	501998000	541224122	657957821	186991	SRX24015860	SRS20810989	SRA1830778	MPI for heart and lung research	MPI for heart and lung research							B	usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Germany	2024-03-21	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");;