metadata: run_metadata: 67 rows where experiment.library_selection = "Oligo-dT", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation

67 rows where experiment.library_selection = "Oligo-dT", experiment.library_source = "TRANSCRIPTOMIC" 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	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	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.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
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
15017	15017	ERR12352459	ERX11729321	ERS17282126	ERP155844	PRJEB70944	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	E-MTAB-13603	Transcriptome Analysis	Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration.	ENA FIRST PUBLIC:2023 12 20\|ENA LAST UPDATE:2023 12 20	Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR	Trpc6a KO sham 3	SAMEA114857167	Institut de Génomique Fonctionnelle	ENA FIRST PUBLIC:2023 12 20T00:27:16Z\|ENA LAST UPDATE:2023 12 20T00:27:16Z\|External Id:SAMEA114857167\|INSDC center name:Institut de Génomique Fonctionnelle\|INSDC first public:2023 12 20T00:27:16Z\|INSDC last update:2023 12 20T00:27:16Z\|INSDC status:public\|Submitter Id:E MTAB 13603:Trpc6a KO sham 3\|age:6\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:Trpc6a knockout\|geographic location country and/or sea:not collected\|individual:5 pooled hearts\|injury:sham operated\|isolate:not applicable\|organism part:heart\|sample name:E MTAB 13603:Trpc6a KO sham 3\|scientific name:Danio rerio\|sex:mix of males and females\|strain:AB	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	E MTAB 13603:Trpc6a KO sham 3 p	Trpc6a KO sham 3 p	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP155844	Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	ENA FIRST PUBLIC:2023 12 20\|ENA LAST UPDATE:2023 12 20	3-Trpc6-KO-sham_R1_001.fastq.gz 3-Trpc6-KO-sham_R2_001.fastq.gz	fastq fastq	9486677705.0	33558571.0	E MTAB 13603:3 Trpc6 KO sham R	0:141.09 1:141.60	A:2537673665;C:2192877777;G:2224713939;T:2525303945;N:6108379	141	141	2537673665	2192877777	2224713939	2525303945	6108379	ERX11729321	ERS17282126	ERA27710226	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive	2	0.95729	0.95618	0.07289	0.07124	0.7725	0.77481	0.52646	0.53221	149	150	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	unknown	unknown	United Kingdom	2023-12-20	Adult	Adult	Heart	Cardiovascular System
15018	15018	ERR12352449	ERX11729311	ERS17282116	ERP155844	PRJEB70944	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	E-MTAB-13603	Transcriptome Analysis	Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration.	ENA FIRST PUBLIC:2023 12 20\|ENA LAST UPDATE:2023 12 20	Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR	Control 7dpa 1	SAMEA114857157	Institut de Génomique Fonctionnelle	ENA FIRST PUBLIC:2023 12 20T00:27:16Z\|ENA LAST UPDATE:2023 12 20T00:27:16Z\|External Id:SAMEA114857157\|INSDC center name:Institut de Génomique Fonctionnelle\|INSDC first public:2023 12 20T00:27:16Z\|INSDC last update:2023 12 20T00:27:16Z\|INSDC status:public\|Submitter Id:E MTAB 13603:Control 7dpa 1\|age:6\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|individual:5 pooled hearts\|injury:cardiac resection\|isolate:not applicable\|organism part:heart\|sample name:E MTAB 13603:Control 7dpa 1\|scientific name:Danio rerio\|sex:mix of males and females\|strain:AB	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	E MTAB 13603:Control 7dpa 1 p	Control 7dpa 1 p	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP155844	Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	ENA FIRST PUBLIC:2023 12 20\|ENA LAST UPDATE:2023 12 20	4-Control-7dpa_R2_001.fastq.gz 4-Control-7dpa_R1_001.fastq.gz	fastq fastq	6795430724.0	23938740.0	E MTAB 13603:4 Control 7dpa R	0:141.55 1:142.32	A:1815845541;C:1567718020;G:1597570908;T:1808008628;N:6287627	141	142	1815845541	1567718020	1597570908	1808008628	6287627	ERX11729311	ERS17282116	ERA27710226	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive	2	0.94648	0.94563	0.09062	0.08917	0.75087	0.75333	0.52273	0.51959	149	150	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	unknown	unknown	United Kingdom	2023-12-20	Adult	Adult	Heart	Cardiovascular System
15019	15019	ERR12352452	ERX11729314	ERS17282119	ERP155844	PRJEB70944	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	E-MTAB-13603	Transcriptome Analysis	Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration.	ENA FIRST PUBLIC:2023 12 20\|ENA LAST UPDATE:2023 12 20	Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR	Control sham 1	SAMEA114857160	Institut de Génomique Fonctionnelle	ENA FIRST PUBLIC:2023 12 20T00:27:16Z\|ENA LAST UPDATE:2023 12 20T00:27:16Z\|External Id:SAMEA114857160\|INSDC center name:Institut de Génomique Fonctionnelle\|INSDC first public:2023 12 20T00:27:16Z\|INSDC last update:2023 12 20T00:27:16Z\|INSDC status:public\|Submitter Id:E MTAB 13603:Control sham 1\|age:6\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|individual:5 pooled hearts\|injury:sham operated\|isolate:not applicable\|organism part:heart\|sample name:E MTAB 13603:Control sham 1\|scientific name:Danio rerio\|sex:mix of males and females\|strain:AB	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	E MTAB 13603:Control sham 1 p	Control sham 1 p	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP155844	Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	ENA FIRST PUBLIC:2023 12 20\|ENA LAST UPDATE:2023 12 20	1-Control-sham_R1_001.fastq.gz 1-Control-sham_R2_001.fastq.gz	fastq fastq	15636676800.0	52122256.0	E MTAB 13603:1 Control sham R	0:150 1:150	A:4263031098;C:3519985187;G:3706349796;T:4147090133;N:220586	150	150	4263031098	3519985187	3706349796	4147090133	220586	ERX11729314	ERS17282119	ERA27710226	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive	2	0.94648	0.94897	0.06005	0.05942	0.76712	0.76822	0.51256	0.50643	150	150	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	unknown	unknown	United Kingdom	2023-12-20	Adult	Adult	Heart	Cardiovascular System
15020	15020	ERR12352451	ERX11729313	ERS17282118	ERP155844	PRJEB70944	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	E-MTAB-13603	Transcriptome Analysis	Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration.	ENA FIRST PUBLIC:2023 12 20\|ENA LAST UPDATE:2023 12 20	Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR	Control 7dpa 3	SAMEA114857159	Institut de Génomique Fonctionnelle	ENA FIRST PUBLIC:2023 12 20T00:27:16Z\|ENA LAST UPDATE:2023 12 20T00:27:16Z\|External Id:SAMEA114857159\|INSDC center name:Institut de Génomique Fonctionnelle\|INSDC first public:2023 12 20T00:27:16Z\|INSDC last update:2023 12 20T00:27:16Z\|INSDC status:public\|Submitter Id:E MTAB 13603:Control 7dpa 3\|age:6\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|individual:5 pooled hearts\|injury:cardiac resection\|isolate:not applicable\|organism part:heart\|sample name:E MTAB 13603:Control 7dpa 3\|scientific name:Danio rerio\|sex:mix of males and females\|strain:AB	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	E MTAB 13603:Control 7dpa 3 p	Control 7dpa 3 p	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP155844	Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	ENA FIRST PUBLIC:2023 12 20\|ENA LAST UPDATE:2023 12 20	6-Control-7dpa_R1_001.fastq.gz 6-Control-7dpa_R2_001.fastq.gz	fastq fastq	8220300600.0	27401002.0	E MTAB 13603:6 Control 7dpa R	0:150 1:150	A:2242736911;C:1858506669;G:1911004513;T:2207938253;N:114254	150	150	2242736911	1858506669	1911004513	2207938253	114254	ERX11729313	ERS17282118	ERA27710226	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive	2	0.94374	0.94281	0.07308	0.07247	0.74028	0.7418	0.50319	0.50503	150	150	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	unknown	unknown	United Kingdom	2023-12-20	Adult	Adult	Heart	Cardiovascular System
15021	15021	ERR12352457	ERX11729319	ERS17282124	ERP155844	PRJEB70944	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	E-MTAB-13603	Transcriptome Analysis	Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration.	ENA FIRST PUBLIC:2023 12 20\|ENA LAST UPDATE:2023 12 20	Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR	Trpc6a KO sham 1	SAMEA114857165	Institut de Génomique Fonctionnelle	ENA FIRST PUBLIC:2023 12 20T00:27:16Z\|ENA LAST UPDATE:2023 12 20T00:27:16Z\|External Id:SAMEA114857165\|INSDC center name:Institut de Génomique Fonctionnelle\|INSDC first public:2023 12 20T00:27:16Z\|INSDC last update:2023 12 20T00:27:16Z\|INSDC status:public\|Submitter Id:E MTAB 13603:Trpc6a KO sham 1\|age:6\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:Trpc6a knockout\|geographic location country and/or sea:not collected\|individual:5 pooled hearts\|injury:sham operated\|isolate:not applicable\|organism part:heart\|sample name:E MTAB 13603:Trpc6a KO sham 1\|scientific name:Danio rerio\|sex:mix of males and females\|strain:AB	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	E MTAB 13603:Trpc6a KO sham 1 p	Trpc6a KO sham 1 p	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP155844	Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	ENA FIRST PUBLIC:2023 12 20\|ENA LAST UPDATE:2023 12 20	1-Trpc6-KO-sham_R1_001.fastq.gz 1-Trpc6-KO-sham_R2_001.fastq.gz	fastq fastq	16463891400.0	54879638.0	E MTAB 13603:1 Trpc6 KO sham R	0:150 1:150	A:4481016793;C:3727761629;G:3905685351;T:4349193797;N:233830	150	150	4481016793	3727761629	3905685351	4349193797	233830	ERX11729319	ERS17282124	ERA27710226	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive	2	0.95234	0.95051	0.05908	0.05789	0.77477	0.77605	0.49876	0.50128	150	150	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	unknown	unknown	United Kingdom	2023-12-20	Adult	Adult	Heart	Cardiovascular System
15022	15022	ERR12352458	ERX11729320	ERS17282125	ERP155844	PRJEB70944	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	E-MTAB-13603	Transcriptome Analysis	Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration.	ENA FIRST PUBLIC:2023 12 20\|ENA LAST UPDATE:2023 12 20	Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR	Trpc6a KO sham 2	SAMEA114857166	Institut de Génomique Fonctionnelle	ENA FIRST PUBLIC:2023 12 20T00:27:16Z\|ENA LAST UPDATE:2023 12 20T00:27:16Z\|External Id:SAMEA114857166\|INSDC center name:Institut de Génomique Fonctionnelle\|INSDC first public:2023 12 20T00:27:16Z\|INSDC last update:2023 12 20T00:27:16Z\|INSDC status:public\|Submitter Id:E MTAB 13603:Trpc6a KO sham 2\|age:6\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:Trpc6a knockout\|geographic location country and/or sea:not collected\|individual:5 pooled hearts\|injury:sham operated\|isolate:not applicable\|organism part:heart\|sample name:E MTAB 13603:Trpc6a KO sham 2\|scientific name:Danio rerio\|sex:mix of males and females\|strain:AB	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	E MTAB 13603:Trpc6a KO sham 2 p	Trpc6a KO sham 2 p	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP155844	Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	ENA FIRST PUBLIC:2023 12 20\|ENA LAST UPDATE:2023 12 20	2-Trpc6-KO-sham_R1_001.fastq.gz 2-Trpc6-KO-sham_R2_001.fastq.gz	fastq fastq	10449824700.0	34832749.0	E MTAB 13603:2 Trpc6 KO sham R	0:150 1:150	A:2842222574;C:2368784549;G:2449245548;T:2789428695;N:143334	150	150	2842222574	2368784549	2449245548	2789428695	143334	ERX11729320	ERS17282125	ERA27710226	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive	2	0.9539	0.95284	0.05851	0.05781	0.77425	0.77656	0.50514	0.50462	150	150	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	unknown	unknown	United Kingdom	2023-12-20	Adult	Adult	Heart	Cardiovascular System
15023	15023	ERR12352453	ERX11729315	ERS17282120	ERP155844	PRJEB70944	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	E-MTAB-13603	Transcriptome Analysis	Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration.	ENA FIRST PUBLIC:2023 12 20\|ENA LAST UPDATE:2023 12 20	Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR	Control sham 2	SAMEA114857161	Institut de Génomique Fonctionnelle	ENA FIRST PUBLIC:2023 12 20T00:27:16Z\|ENA LAST UPDATE:2023 12 20T00:27:16Z\|External Id:SAMEA114857161\|INSDC center name:Institut de Génomique Fonctionnelle\|INSDC first public:2023 12 20T00:27:16Z\|INSDC last update:2023 12 20T00:27:16Z\|INSDC status:public\|Submitter Id:E MTAB 13603:Control sham 2\|age:6\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|individual:5 pooled hearts\|injury:sham operated\|isolate:not applicable\|organism part:heart\|sample name:E MTAB 13603:Control sham 2\|scientific name:Danio rerio\|sex:mix of males and females\|strain:AB	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	E MTAB 13603:Control sham 2 p	Control sham 2 p	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP155844	Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	ENA FIRST PUBLIC:2023 12 20\|ENA LAST UPDATE:2023 12 20	2-Control-sham_R1_001.fastq.gz 2-Control-sham_R2_001.fastq.gz	fastq fastq	13714149300.0	45713831.0	E MTAB 13603:2 Control sham R	0:150 1:150	A:3744799859;C:3102314317;G:3246683965;T:3620157056;N:194103	150	150	3744799859	3102314317	3246683965	3620157056	194103	ERX11729315	ERS17282120	ERA27710226	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive	2	0.94672	0.94688	0.05944	0.05917	0.76654	0.76773	0.51792	0.51959	150	150	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	unknown	unknown	United Kingdom	2023-12-20	Adult	Adult	Heart	Cardiovascular System
15024	15024	ERR12352450	ERX11729312	ERS17282117	ERP155844	PRJEB70944	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	E-MTAB-13603	Transcriptome Analysis	Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration.	ENA FIRST PUBLIC:2023 12 20\|ENA LAST UPDATE:2023 12 20	Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR	Control 7dpa 2	SAMEA114857158	Institut de Génomique Fonctionnelle	ENA FIRST PUBLIC:2023 12 20T00:27:16Z\|ENA LAST UPDATE:2023 12 20T00:27:16Z\|External Id:SAMEA114857158\|INSDC center name:Institut de Génomique Fonctionnelle\|INSDC first public:2023 12 20T00:27:16Z\|INSDC last update:2023 12 20T00:27:16Z\|INSDC status:public\|Submitter Id:E MTAB 13603:Control 7dpa 2\|age:6\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|geographic location country and/or sea:not collected\|individual:5 pooled hearts\|injury:cardiac resection\|isolate:not applicable\|organism part:heart\|sample name:E MTAB 13603:Control 7dpa 2\|scientific name:Danio rerio\|sex:mix of males and females\|strain:AB	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	E MTAB 13603:Control 7dpa 2 p	Control 7dpa 2 p	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP155844	Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	ENA FIRST PUBLIC:2023 12 20\|ENA LAST UPDATE:2023 12 20	5-Control-7dpa_R1_001.fastq.gz 5-Control-7dpa_R2_001.fastq.gz	fastq fastq	9830629200.0	32768764.0	E MTAB 13603:5 Control 7dpa R	0:150 1:150	A:2655376287;C:2237942590;G:2372252275;T:2564920802;N:137246	150	150	2655376287	2237942590	2372252275	2564920802	137246	ERX11729312	ERS17282117	ERA27710226	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive	2	0.94476	0.94389	0.06625	0.06506	0.74197	0.7441	0.50589	0.50685	150	150	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	unknown	unknown	United Kingdom	2023-12-20	Adult	Adult	Heart	Cardiovascular System
15025	15025	ERR12352454	ERX11729316	ERS17282121	ERP155844	PRJEB70944	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	E-MTAB-13603	Transcriptome Analysis	Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration.	ENA FIRST PUBLIC:2023 12 20\|ENA LAST UPDATE:2023 12 20	Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR	Trpc6a KO 7dpa 1	SAMEA114857162	Institut de Génomique Fonctionnelle	ENA FIRST PUBLIC:2023 12 20T00:27:16Z\|ENA LAST UPDATE:2023 12 20T00:27:16Z\|External Id:SAMEA114857162\|INSDC center name:Institut de Génomique Fonctionnelle\|INSDC first public:2023 12 20T00:27:16Z\|INSDC last update:2023 12 20T00:27:16Z\|INSDC status:public\|Submitter Id:E MTAB 13603:Trpc6a KO 7dpa 1\|age:6\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:Trpc6a knockout\|geographic location country and/or sea:not collected\|individual:5 pooled hearts\|injury:cardiac resection\|isolate:not applicable\|organism part:heart\|sample name:E MTAB 13603:Trpc6a KO 7dpa 1\|scientific name:Danio rerio\|sex:mix of males and females\|strain:AB	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	E MTAB 13603:Trpc6a KO 7dpa 1 p	Trpc6a KO 7dpa 1 p	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP155844	Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	ENA FIRST PUBLIC:2023 12 20\|ENA LAST UPDATE:2023 12 20	4-Trpc6-KO-7dpa_R2_001.fastq.gz 4-Trpc6-KO-7dpa_R1_001.fastq.gz	fastq fastq	5379338700.0	17931129.0	E MTAB 13603:4 Trpc6 KO 7dpa R	0:150 1:150	A:1451310854;C:1236467303;G:1283161720;T:1408322640;N:76183	150	150	1451310854	1236467303	1283161720	1408322640	76183	ERX11729316	ERS17282121	ERA27710226	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive	2	0.94369	0.94789	0.06027	0.06036	0.74647	0.74649	0.4767	0.50107	150	150	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	unknown	unknown	United Kingdom	2023-12-20	Adult	Adult	Heart	Cardiovascular System
15026	15026	ERR12352455	ERX11729317	ERS17282122	ERP155844	PRJEB70944	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	E-MTAB-13603	Transcriptome Analysis	Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration.	ENA FIRST PUBLIC:2023 12 20\|ENA LAST UPDATE:2023 12 20	Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR	Trpc6a KO 7dpa 2	SAMEA114857163	Institut de Génomique Fonctionnelle	ENA FIRST PUBLIC:2023 12 20T00:27:16Z\|ENA LAST UPDATE:2023 12 20T00:27:16Z\|External Id:SAMEA114857163\|INSDC center name:Institut de Génomique Fonctionnelle\|INSDC first public:2023 12 20T00:27:16Z\|INSDC last update:2023 12 20T00:27:16Z\|INSDC status:public\|Submitter Id:E MTAB 13603:Trpc6a KO 7dpa 2\|age:6\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:Trpc6a knockout\|geographic location country and/or sea:not collected\|individual:5 pooled hearts\|injury:cardiac resection\|isolate:not applicable\|organism part:heart\|sample name:E MTAB 13603:Trpc6a KO 7dpa 2\|scientific name:Danio rerio\|sex:mix of males and females\|strain:AB	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	E MTAB 13603:Trpc6a KO 7dpa 2 p	Trpc6a KO 7dpa 2 p	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP155844	Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	ENA FIRST PUBLIC:2023 12 20\|ENA LAST UPDATE:2023 12 20	5-Trpc6-KO-7dpa_R2_001.fastq.gz 5-Trpc6-KO-7dpa_R1_001.fastq.gz	fastq fastq	14033980200.0	46779934.0	E MTAB 13603:5 Trpc6 KO 7dpa R	0:150 1:150	A:3810908166;C:3197374649;G:3343702230;T:3681798453;N:196702	150	150	3810908166	3197374649	3343702230	3681798453	196702	ERX11729317	ERS17282122	ERA27710226	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive	2	0.94801	0.94661	0.06342	0.06201	0.74834	0.75207	0.50789	0.5027	150	150	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	unknown	unknown	United Kingdom	2023-12-20	Adult	Adult	Heart	Cardiovascular System
15027	15027	ERR12352456	ERX11729318	ERS17282123	ERP155844	PRJEB70944	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	E-MTAB-13603	Transcriptome Analysis	Myocardial damage caused for example by cardiac ischemia leads to ventricular volume overload resulting in increased stretch of the remaining myocardium. In adult mammals these changes trigger an adaptive cardiomyocyte hypertrophic response which if the damage is extensive will ultimately lead to pathological hypertrophy and heart failure. Conversely in response to extensive myocardial damage cardiomyocytes in the adult zebrafish heart and neonatal mice proliferate and completely regenerate the damaged myocardium. We therefore hypothesized that in adult zebrafish changes in mechanical loading due to myocardial damage may act as a trigger to induce cardiac regeneration. Based on this notion we sought to identify mechanosensors which could be involved in detecting changes in mechanical loading and triggering regeneration. Here we show using a combination of knockout animals RNAseq and in vitro assays that the mechanosensitive ion channel Trpc6a is required by cardiomyocytes for successful cardiac regeneration in adult zebrafish. Furthermore using a cyclic cell stretch assay we have determined that Trpc6a induces the expression of components of the AP1 transcription complex in response to mechanical stretch. Our data highlights how changes in mechanical forces due to myocardial damage can be detected by mechanosensors which in turn can trigger cardiac regeneration.	ENA FIRST PUBLIC:2023 12 20\|ENA LAST UPDATE:2023 12 20	Protocols: Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR	Trpc6a KO 7dpa 3	SAMEA114857164	Institut de Génomique Fonctionnelle	ENA FIRST PUBLIC:2023 12 20T00:27:16Z\|ENA LAST UPDATE:2023 12 20T00:27:16Z\|External Id:SAMEA114857164\|INSDC center name:Institut de Génomique Fonctionnelle\|INSDC first public:2023 12 20T00:27:16Z\|INSDC last update:2023 12 20T00:27:16Z\|INSDC status:public\|Submitter Id:E MTAB 13603:Trpc6a KO 7dpa 3\|age:6\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:adult\|genotype:Trpc6a knockout\|geographic location country and/or sea:not collected\|individual:5 pooled hearts\|injury:cardiac resection\|isolate:not applicable\|organism part:heart\|sample name:E MTAB 13603:Trpc6a KO 7dpa 3\|scientific name:Danio rerio\|sex:mix of males and females\|strain:AB	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	E MTAB 13603:Trpc6a KO 7dpa 3 p	Trpc6a KO 7dpa 3 p	The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	Adult fish were anesthetized in Tricaine. Each group trpc6a KO and Control consists of 3 biological replicates of 5 pooled hearts For each replicate 5 hearts were pooled and RNA was extracted using Trizol/choloform The RNA sequencing library preparation was performed by using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions NEB Ipswich MA USA. Briefly mRNAs were first enriched with OligodT beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at three primeends and universal adapters were ligated to cDNA fragments followed by index addition and library enrichment by limited cycle PCR		RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP155844	Illumina NovaSeq 6000 paired end sequencing; The ion channel Trpc6a regulates the cardiomyocyte regenerative response to mechanical stretch	ENA FIRST PUBLIC:2023 12 20\|ENA LAST UPDATE:2023 12 20	6-Trpc6-KO-7dpa_R2_001.fastq.gz 6-Trpc6-KO-7dpa_R1_001.fastq.gz	fastq fastq	10056041651.0	35562752.0	E MTAB 13603:6 Trpc6 KO 7dpa R	0:141.00 1:141.77	A:2670755890;C:2335065805;G:2381199297;T:2659552078;N:9468581	141	141	2670755890	2335065805	2381199297	2659552078	9468581	ERX11729318	ERS17282123	ERA27710226	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive	2	0.95324	0.9515	0.07632	0.07479	0.75597	0.75787	0.51981	0.52087	113	113	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	unknown	unknown	United Kingdom	2023-12-20	Adult	Adult	Heart	Cardiovascular System
31994	31994	SRR28906400	SRX24462857	SRS21215803	SRP505889	PRJNA1108009	Danio rerio Raw sequence reads	PRJNA1108009	Whole Genome Sequencing	cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome				H KO 1dpt 1		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:3mpf\|dev stage:Adult\|collection date:2023 08\|geo loc name:China:wuhan\|sex:male\|tissue:heart\|lat lon:30.56 N 114.45 E\|BioSampleModel:Model organism or animal	RNA seq of danio rario:adult male heart	H KO 1dpt 1	H KO 1dpt 1	normal RNA seq of Danio rerio			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505889			H-KO-1dpt-1_2.fq.gz H-KO-1dpt-1_1.fq.gz	fastq fastq	7562116200.0	25207054.0	H KO 1dpt 1 1.fq.gz	0:150 1:150	A:2053051017;C:1729576392;G:1752482225;T:2025170234;N:1836332	150	150	2053051017	1729576392	1752482225	2025170234	1836332	SRX24462857	SRS21215803	SRA1859838	Wuhan University\|Taikang Medical School (School of Basic Medical Sc	Wuhan University	2	0.94384	0.94341	0.0998	0.09865	0.71433	0.71427	0.49335	0.49672	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-06	Adult	Adult	Heart	Cardiovascular System
31995	31995	SRR28906401	SRX24462856	SRS21215806	SRP505889	PRJNA1108009	Danio rerio Raw sequence reads	PRJNA1108009	Whole Genome Sequencing	cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome				H WT 1dpt 3		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:3mpf\|dev stage:Adult\|collection date:2023 08\|geo loc name:China:wuhan\|sex:male\|tissue:heart\|lat lon:30.56 N 114.44 E\|BioSampleModel:Model organism or animal	RNA seq of danio rario:adult male heart	H WT 1dpt 3	H WT 1dpt 3	normal RNA seq of Danio rerio			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505889			H-WT-1dpt-3_1.fq.gz H-WT-1dpt-3_2.fq.gz	fastq fastq	7976703000.0	26589010.0	H WT 1dpt 3 1.fq.gz	0:150 1:150	A:2168595183;C:1821923593;G:1848475154;T:2135714236;N:1994834	150	150	2168595183	1821923593	1848475154	2135714236	1994834	SRX24462856	SRS21215806	SRA1859838	Wuhan University\|Taikang Medical School (School of Basic Medical Sc	Wuhan University	2	0.94335	0.9438	0.10093	0.10044	0.7122	0.71031	0.50824	0.51139	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-06	Adult	Adult	Heart	Cardiovascular System
31996	31996	SRR28906402	SRX24462855	SRS21215805	SRP505889	PRJNA1108009	Danio rerio Raw sequence reads	PRJNA1108009	Whole Genome Sequencing	cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome				H WT 1dpt 2		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:3mpf\|dev stage:Adult\|collection date:2023 08\|geo loc name:China:wuhan\|sex:male\|tissue:heart\|lat lon:30.56 N 114.43 E\|BioSampleModel:Model organism or animal	RNA seq of danio rario:adult male heart	H WT 1dpt 2	H WT 1dpt 2	normal RNA seq of Danio rerio			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505889			H-WT-1dpt-2_2.fq.gz H-WT-1dpt-2_1.fq.gz	fastq fastq	7656200400.0	25520668.0	H WT 1dpt 2 1.fq.gz	0:150 1:150	A:2082823123;C:1745563595;G:1770285873;T:2055608172;N:1919637	150	150	2082823123	1745563595	1770285873	2055608172	1919637	SRX24462855	SRS21215805	SRA1859838	Wuhan University\|Taikang Medical School (School of Basic Medical Sc	Wuhan University	2	0.9435	0.94385	0.1003	0.10068	0.71015	0.70956	0.51199	0.51323	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-06	Adult	Adult	Heart	Cardiovascular System
31997	31997	SRR28906403	SRX24462854	SRS21215800	SRP505889	PRJNA1108009	Danio rerio Raw sequence reads	PRJNA1108009	Whole Genome Sequencing	cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome				H WT 1dpt 1		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:3mpf\|dev stage:Adult\|collection date:2023 08\|geo loc name:China:wuhan\|sex:male\|tissue:heart\|lat lon:30.56 N 114.42 E\|BioSampleModel:Model organism or animal	RNA seq of danio rario:adult male heart	H WT 1dpt 1	H WT 1dpt 1	normal RNA seq of Danio rerio			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505889			H-WT-1dpt-1_1.fq.gz H-WT-1dpt-1_2.fq.gz	fastq fastq	7762317300.0	25874391.0	H WT 1dpt 1 1.fq.gz	0:150 1:150	A:2110489933;C:1771640570;G:1794995113;T:2083336499;N:1855185	150	150	2110489933	1771640570	1794995113	2083336499	1855185	SRX24462854	SRS21215800	SRA1859838	Wuhan University\|Taikang Medical School (School of Basic Medical Sc	Wuhan University	2	0.94438	0.94341	0.0996	0.09862	0.70989	0.70952	0.51628	0.50961	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-06	Adult	Adult	Heart	Cardiovascular System
31998	31998	SRR28906404	SRX24462853	SRS21215801	SRP505889	PRJNA1108009	Danio rerio Raw sequence reads	PRJNA1108009	Whole Genome Sequencing	cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome				H KO UI 3		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:3mpf\|dev stage:Adult\|collection date:2023 08\|geo loc name:China:wuhan\|sex:male\|tissue:heart\|lat lon:30.56 N 114.41 E\|BioSampleModel:Model organism or animal	RNA seq of danio rario:adult male heart	H KO UI 3	H KO UI 3	normal RNA seq of Danio rerio			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505889			H-KO-UI-3_1.fq.gz H-KO-UI-3_2.fq.gz	fastq fastq	8074894200.0	26916314.0	H KO UI 3 1.fq.gz	0:150 1:150	A:2188747586;C:1844507036;G:1872467804;T:2167174432;N:1997342	150	150	2188747586	1844507036	1872467804	2167174432	1997342	SRX24462853	SRS21215801	SRA1859838	Wuhan University\|Taikang Medical School (School of Basic Medical Sc	Wuhan University	2	0.94616	0.9458	0.08568	0.08577	0.72163	0.72127	0.49125	0.49327	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-06	Adult	Adult	Heart	Cardiovascular System
31999	31999	SRR28906405	SRX24462852	SRS21215802	SRP505889	PRJNA1108009	Danio rerio Raw sequence reads	PRJNA1108009	Whole Genome Sequencing	cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome				H KO UI 2		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:3mpf\|dev stage:Adult\|collection date:2023 08\|geo loc name:China:wuhan\|sex:male\|tissue:heart\|lat lon:30.56 N 114.40 E\|BioSampleModel:Model organism or animal	RNA seq of danio rario:adult male heart	H KO UI 2	H KO UI 2	normal RNA seq of Danio rerio			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505889			H-KO-UI-2_1.fq.gz H-KO-UI-2_2.fq.gz	fastq fastq	7322976300.0	24409921.0	H KO UI 2 1.fq.gz	0:150 1:150	A:1977575170;C:1682113004;G:1705811265;T:1955632804;N:1844057	150	150	1977575170	1682113004	1705811265	1955632804	1844057	SRX24462852	SRS21215802	SRA1859838	Wuhan University\|Taikang Medical School (School of Basic Medical Sc	Wuhan University	2	0.94609	0.94626	0.08289	0.08343	0.72251	0.72206	0.47771	0.48416	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-06	Adult	Adult	Heart	Cardiovascular System
32000	32000	SRR28906406	SRX24462851	SRS21215799	SRP505889	PRJNA1108009	Danio rerio Raw sequence reads	PRJNA1108009	Whole Genome Sequencing	cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome				H KO UI 1		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:3mpf\|dev stage:Adult\|collection date:2023 08\|geo loc name:China:wuhan\|sex:male\|tissue:heart\|lat lon:30.56 N 114.39 E\|BioSampleModel:Model organism or animal	RNA seq of danio rario:adult male heart	H KO UI 1	H KO UI 1	normal RNA seq of Danio rerio			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505889			H-KO-UI-1_1.fq.gz H-KO-UI-1_2.fq.gz	fastq fastq	7719372900.0	25731243.0	H KO UI 1 1.fq.gz	0:150 1:150	A:2090530132;C:1765932073;G:1794848389;T:2066130430;N:1931876	150	150	2090530132	1765932073	1794848389	2066130430	1931876	SRX24462851	SRS21215799	SRA1859838	Wuhan University\|Taikang Medical School (School of Basic Medical Sc	Wuhan University	2	0.94579	0.94669	0.08477	0.08495	0.72224	0.72149	0.47982	0.48098	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-06	Adult	Adult	Heart	Cardiovascular System
32001	32001	SRR28906407	SRX24462850	SRS21215798	SRP505889	PRJNA1108009	Danio rerio Raw sequence reads	PRJNA1108009	Whole Genome Sequencing	cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome				H KO 7dpt 3		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:3mpf\|dev stage:Adult\|collection date:2023 08\|geo loc name:China:wuhan\|sex:male\|tissue:heart\|lat lon:30.56 N 114.59 E\|BioSampleModel:Model organism or animal	RNA seq of danio rario:adult male heart	H KO 7dpt 3	H KO 7dpt 3	normal RNA seq of Danio rerio			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505889			H-KO-7dpt-3_1.fq.gz H-KO-7dpt-3_2.fq.gz	fastq fastq	8751619200.0	29172064.0	H KO 7dpt 3 1.fq.gz	0:150 1:150	A:2378357776;C:1995299013;G:2022275849;T:2353549435;N:2137127	150	150	2378357776	1995299013	2022275849	2353549435	2137127	SRX24462850	SRS21215798	SRA1859838	Wuhan University\|Taikang Medical School (School of Basic Medical Sc	Wuhan University	2	0.94284	0.94237	0.10245	0.10267	0.71534	0.71522	0.48671	0.48061	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-06	Adult	Adult	Heart	Cardiovascular System
32002	32002	SRR28906408	SRX24462849	SRS21215797	SRP505889	PRJNA1108009	Danio rerio Raw sequence reads	PRJNA1108009	Whole Genome Sequencing	cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome				H KO 7dpt 2		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:3mpf\|dev stage:Adult\|collection date:2023 08\|geo loc name:China:wuhan\|sex:male\|tissue:heart\|lat lon:30.56 N 114.58 E\|BioSampleModel:Model organism or animal	RNA seq of danio rario:adult male heart	H KO 7dpt 2	H KO 7dpt 2	normal RNA seq of Danio rerio			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505889			H-KO-7dpt-2_2.fq.gz H-KO-7dpt-2_1.fq.gz	fastq fastq	8704213200.0	29014044.0	H KO 7dpt 2 1.fq.gz	0:150 1:150	A:2361470638;C:1987488058;G:2014448011;T:2338898652;N:1907841	150	150	2361470638	1987488058	2014448011	2338898652	1907841	SRX24462849	SRS21215797	SRA1859838	Wuhan University\|Taikang Medical School (School of Basic Medical Sc	Wuhan University	2	0.94331	0.94387	0.10094	0.10045	0.71536	0.71356	0.48579	0.48959	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-06	Adult	Adult	Heart	Cardiovascular System
32003	32003	SRR28906409	SRX24462848	SRS21215793	SRP505889	PRJNA1108009	Danio rerio Raw sequence reads	PRJNA1108009	Whole Genome Sequencing	cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome				H KO 7dpt 1		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:3mpf\|dev stage:Adult\|collection date:2023 08\|geo loc name:China:wuhan\|sex:male\|tissue:heart\|lat lon:30.56 N 114.57 E\|BioSampleModel:Model organism or animal	RNA seq of danio rario:adult male heart	H KO 7dpt 1	H KO 7dpt 1	normal RNA seq of Danio rerio			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505889			H-KO-7dpt-1_1.fq.gz H-KO-7dpt-1_2.fq.gz	fastq fastq	8217376500.0	27391255.0	H KO 7dpt 1 1.fq.gz	0:150 1:150	A:2225497058;C:1878586733;G:1906220197;T:2205098635;N:1973877	150	150	2225497058	1878586733	1906220197	2205098635	1973877	SRX24462848	SRS21215793	SRA1859838	Wuhan University\|Taikang Medical School (School of Basic Medical Sc	Wuhan University	2	0.94328	0.94383	0.10058	0.10047	0.71256	0.71141	0.47543	0.4729	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-06	Adult	Adult	Heart	Cardiovascular System
32004	32004	SRR28906410	SRX24462847	SRS21215792	SRP505889	PRJNA1108009	Danio rerio Raw sequence reads	PRJNA1108009	Whole Genome Sequencing	cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome				H WT 7dpt 3		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:3mpf\|dev stage:Adult\|collection date:2023 08\|geo loc name:China:wuhan\|sex:male\|tissue:heart\|lat lon:30.56 N 114.56 E\|BioSampleModel:Model organism or animal	RNA seq of danio rario:adult male heart	H WT 7dpt 3	H WT 7dpt 3	normal RNA seq of Danio rerio			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505889			H-WT-7dpt-3_1.fq.gz H-WT-7dpt-3_2.fq.gz	fastq fastq	8481387900.0	28271293.0	H WT 7dpt 3 1.fq.gz	0:150 1:150	A:2299162401;C:1934779265;G:1965090511;T:2280371695;N:1984028	150	150	2299162401	1934779265	1965090511	2280371695	1984028	SRX24462847	SRS21215792	SRA1859838	Wuhan University\|Taikang Medical School (School of Basic Medical Sc	Wuhan University	2	0.94277	0.94304	0.1044	0.10406	0.71912	0.71916	0.48211	0.48332	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-06	Adult	Adult	Heart	Cardiovascular System
32005	32005	SRR28906411	SRX24462846	SRS21215794	SRP505889	PRJNA1108009	Danio rerio Raw sequence reads	PRJNA1108009	Whole Genome Sequencing	cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome				H WT UI 3		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:3mpf\|dev stage:Adult\|collection date:2023 08\|geo loc name:China:wuhan\|sex:male\|tissue:heart\|lat lon:30.56 N 114.38 E\|BioSampleModel:Model organism or animal	RNA seq of danio rario:adult male heart	H WT UI 3	H WT UI 3	normal RNA seq of Danio rerio			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505889			H-WT-UI-3_1.fq.gz H-WT-UI-3_2.fq.gz	fastq fastq	7688910600.0	25629702.0	H WT UI 3 1.fq.gz	0:150 1:150	A:2097391352;C:1749410635;G:1772959080;T:2067249011;N:1900522	150	150	2097391352	1749410635	1772959080	2067249011	1900522	SRX24462846	SRS21215794	SRA1859838	Wuhan University\|Taikang Medical School (School of Basic Medical Sc	Wuhan University	2	0.94913	0.94883	0.08493	0.08488	0.74391	0.74412	0.49665	0.49102	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-06	Adult	Adult	Heart	Cardiovascular System
32006	32006	SRR28906412	SRX24462845	SRS21215789	SRP505889	PRJNA1108009	Danio rerio Raw sequence reads	PRJNA1108009	Whole Genome Sequencing	cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome				H WT 7dpt 2		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:3mpf\|dev stage:Adult\|collection date:2023 08\|geo loc name:China:wuhan\|sex:male\|tissue:heart\|lat lon:30.56 N 114.55 E\|BioSampleModel:Model organism or animal	RNA seq of danio rario:adult male heart	H WT 7dpt 2	H WT 7dpt 2	normal RNA seq of Danio rerio			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505889			H-WT-7dpt-2_1.fq.gz H-WT-7dpt-2_2.fq.gz	fastq fastq	8122767900.0	27075893.0	H WT 7dpt 2 1.fq.gz	0:150 1:150	A:2209122325;C:1845876653;G:1874400213;T:2191385562;N:1983147	150	150	2209122325	1845876653	1874400213	2191385562	1983147	SRX24462845	SRS21215789	SRA1859838	Wuhan University\|Taikang Medical School (School of Basic Medical Sc	Wuhan University	2	0.94213	0.94221	0.1066	0.10643	0.72143	0.72054	0.47732	0.47973	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-06	Adult	Adult	Heart	Cardiovascular System
32007	32007	SRR28906413	SRX24462844	SRS21215795	SRP505889	PRJNA1108009	Danio rerio Raw sequence reads	PRJNA1108009	Whole Genome Sequencing	cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome				H WT 7dpt 1		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:3mpf\|dev stage:Adult\|collection date:2023 08\|geo loc name:China:wuhan\|sex:male\|tissue:heart\|lat lon:30.56 N 114.54 E\|BioSampleModel:Model organism or animal	RNA seq of danio rario:adult male heart	H WT 7dpt 1	H WT 7dpt 1	normal RNA seq of Danio rerio			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505889			H-WT-7dpt-1_1.fq.gz H-WT-7dpt-1_2.fq.gz	fastq fastq	8528784300.0	28429281.0	H WT 7dpt 1 1.fq.gz	0:150 1:150	A:2315405815;C:1946703478;G:1973240605;T:2291355768;N:2078634	150	150	2315405815	1946703478	1973240605	2291355768	2078634	SRX24462844	SRS21215795	SRA1859838	Wuhan University\|Taikang Medical School (School of Basic Medical Sc	Wuhan University	2	0.94286	0.94346	0.10556	0.10568	0.72129	0.72038	0.48324	0.48088	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-06	Adult	Adult	Heart	Cardiovascular System
32008	32008	SRR28906414	SRX24462843	SRS21215796	SRP505889	PRJNA1108009	Danio rerio Raw sequence reads	PRJNA1108009	Whole Genome Sequencing	cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome				H KO 3dpt 3		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:3mpf\|dev stage:Adult\|collection date:2023 08\|geo loc name:China:wuhan\|sex:male\|tissue:heart\|lat lon:30.56 N 114.53 E\|BioSampleModel:Model organism or animal	RNA seq of danio rario:adult male heart	H KO 3dpt 3	H KO 3dpt 3	normal RNA seq of Danio rerio			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505889			H-KO-3dpt-3_1.fq.gz H-KO-3dpt-3_2.fq.gz	fastq fastq	8342832900.0	27809443.0	H KO 3dpt 3 1.fq.gz	0:150 1:150	A:2266689673;C:1905685494;G:1930305329;T:2238163657;N:1988747	150	150	2266689673	1905685494	1930305329	2238163657	1988747	SRX24462843	SRS21215796	SRA1859838	Wuhan University\|Taikang Medical School (School of Basic Medical Sc	Wuhan University	2	0.94595	0.94499	0.09639	0.09628	0.715	0.71553	0.49016	0.49123	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-06	Adult	Adult	Heart	Cardiovascular System
32009	32009	SRR28906415	SRX24462842	SRS21215791	SRP505889	PRJNA1108009	Danio rerio Raw sequence reads	PRJNA1108009	Whole Genome Sequencing	cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome				H KO 3dpt 2		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:3mpf\|dev stage:Adult\|collection date:2023 08\|geo loc name:China:wuhan\|sex:male\|tissue:heart\|lat lon:30.56 N 114.52 E\|BioSampleModel:Model organism or animal	RNA seq of danio rario:adult male heart	H KO 3dpt 2	H KO 3dpt 2	normal RNA seq of Danio rerio			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505889			H-KO-3dpt-2_1.fq.gz H-KO-3dpt-2_2.fq.gz	fastq fastq	7442766300.0	24809221.0	H KO 3dpt 2 1.fq.gz	0:150 1:150	A:2019309536;C:1702177984;G:1726456407;T:1993008040;N:1814333	150	150	2019309536	1702177984	1726456407	1993008040	1814333	SRX24462842	SRS21215791	SRA1859838	Wuhan University\|Taikang Medical School (School of Basic Medical Sc	Wuhan University	2	0.94586	0.94468	0.09614	0.09561	0.71648	0.71705	0.49676	0.49381	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-06	Adult	Adult	Heart	Cardiovascular System
32010	32010	SRR28906416	SRX24462841	SRS21215788	SRP505889	PRJNA1108009	Danio rerio Raw sequence reads	PRJNA1108009	Whole Genome Sequencing	cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome				H KO 3dpt 1		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:3mpf\|dev stage:Adult\|collection date:2023 08\|geo loc name:China:wuhan\|sex:male\|tissue:heart\|lat lon:30.56 N 114.51 E\|BioSampleModel:Model organism or animal	RNA seq of danio rario:adult male heart	H KO 3dpt 1	H KO 3dpt 1	normal RNA seq of Danio rerio			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505889			H-KO-3dpt-1_1.fq.gz H-KO-3dpt-1_2.fq.gz	fastq fastq	7831293600.0	26104312.0	H KO 3dpt 1 1.fq.gz	0:150 1:150	A:2128253770;C:1787608569;G:1811254103;T:2102258260;N:1918898	150	150	2128253770	1787608569	1811254103	2102258260	1918898	SRX24462841	SRS21215788	SRA1859838	Wuhan University\|Taikang Medical School (School of Basic Medical Sc	Wuhan University	2	0.94613	0.94565	0.09774	0.09695	0.71474	0.71474	0.47983	0.47889	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-06	Adult	Adult	Heart	Cardiovascular System
32011	32011	SRR28906417	SRX24462840	SRS21215790	SRP505889	PRJNA1108009	Danio rerio Raw sequence reads	PRJNA1108009	Whole Genome Sequencing	cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome				H WT 3dpt 3		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:3mpf\|dev stage:Adult\|collection date:2023 08\|geo loc name:China:wuhan\|sex:male\|tissue:heart\|lat lon:30.56 N 114.50 E\|BioSampleModel:Model organism or animal	RNA seq of danio rario:adult male heart	H WT 3dpt 3	H WT 3dpt 3	normal RNA seq of Danio rerio			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505889			H-WT-3dpt-3_1.fq.gz H-WT-3dpt-3_2.fq.gz	fastq fastq	8069992500.0	26899975.0	H WT 3dpt 3 1.fq.gz	0:150 1:150	A:2190393002;C:1843546509;G:1866938814;T:2167244861;N:1869314	150	150	2190393002	1843546509	1866938814	2167244861	1869314	SRX24462840	SRS21215790	SRA1859838	Wuhan University\|Taikang Medical School (School of Basic Medical Sc	Wuhan University	2	0.9433	0.94216	0.09862	0.09804	0.70845	0.70843	0.48894	0.48921	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-06	Adult	Adult	Heart	Cardiovascular System
32012	32012	SRR28906418	SRX24462839	SRS21215786	SRP505889	PRJNA1108009	Danio rerio Raw sequence reads	PRJNA1108009	Whole Genome Sequencing	cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome				H WT 3dpt 2		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:3mpf\|dev stage:Adult\|collection date:2023 08\|geo loc name:China:wuhan\|sex:male\|tissue:heart\|lat lon:30.56 N 114.49 E\|BioSampleModel:Model organism or animal	RNA seq of danio rario:adult male heart	H WT 3dpt 2	H WT 3dpt 2	normal RNA seq of Danio rerio			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505889			H-WT-3dpt-2_1.fq.gz H-WT-3dpt-2_2.fq.gz	fastq fastq	7502274600.0	25007582.0	H WT 3dpt 2 1.fq.gz	0:150 1:150	A:2036169286;C:1712256370;G:1737197102;T:2014865457;N:1786385	150	150	2036169286	1712256370	1737197102	2014865457	1786385	SRX24462839	SRS21215786	SRA1859838	Wuhan University\|Taikang Medical School (School of Basic Medical Sc	Wuhan University	2	0.94174	0.94129	0.09992	0.09885	0.70865	0.70863	0.48713	0.48657	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-06	Adult	Adult	Heart	Cardiovascular System
32013	32013	SRR28906419	SRX24462838	SRS21215787	SRP505889	PRJNA1108009	Danio rerio Raw sequence reads	PRJNA1108009	Whole Genome Sequencing	cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome				H WT 3dpt 1		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:3mpf\|dev stage:Adult\|collection date:2023 08\|geo loc name:China:wuhan\|sex:male\|tissue:heart\|lat lon:30.56 N 114.48 E\|BioSampleModel:Model organism or animal	RNA seq of danio rario:adult male heart	H WT 3dpt 1	H WT 3dpt 1	normal RNA seq of Danio rerio			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505889			H-WT-3dpt-1_1.fq.gz H-WT-3dpt-1_2.fq.gz	fastq fastq	7511851800.0	25039506.0	H WT 3dpt 1 1.fq.gz	0:150 1:150	A:2035709532;C:1717586093;G:1742606776;T:2014155061;N:1794338	150	150	2035709532	1717586093	1742606776	2014155061	1794338	SRX24462838	SRS21215787	SRA1859838	Wuhan University\|Taikang Medical School (School of Basic Medical Sc	Wuhan University	2	0.94269	0.9423	0.0996	0.09902	0.70952	0.70978	0.48839	0.48674	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-06	Adult	Adult	Heart	Cardiovascular System
32014	32014	SRR28906420	SRX24462837	SRS21215785	SRP505889	PRJNA1108009	Danio rerio Raw sequence reads	PRJNA1108009	Whole Genome Sequencing	cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome				H KO 1dpt 3		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:3mpf\|dev stage:Adult\|collection date:2023 08\|geo loc name:China:wuhan\|sex:male\|tissue:heart\|lat lon:30.56 N 114.47 E\|BioSampleModel:Model organism or animal	RNA seq of danio rario:adult male heart	H KO 1dpt 3	H KO 1dpt 3	normal RNA seq of Danio rerio			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505889			H-KO-1dpt-3_1.fq.gz H-KO-1dpt-3_2.fq.gz	fastq fastq	7530376500.0	25101255.0	H KO 1dpt 3 1.fq.gz	0:150 1:150	A:2038997159;C:1723582025;G:1752027912;T:2013934872;N:1834532	150	150	2038997159	1723582025	1752027912	2013934872	1834532	SRX24462837	SRS21215785	SRA1859838	Wuhan University\|Taikang Medical School (School of Basic Medical Sc	Wuhan University	2	0.94529	0.94377	0.09755	0.09638	0.71368	0.71386	0.49782	0.49531	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-06	Adult	Adult	Heart	Cardiovascular System
32015	32015	SRR28906421	SRX24462836	SRS21215783	SRP505889	PRJNA1108009	Danio rerio Raw sequence reads	PRJNA1108009	Whole Genome Sequencing	cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome				H KO 1dpt 2		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:3mpf\|dev stage:Adult\|collection date:2023 08\|geo loc name:China:wuhan\|sex:male\|tissue:heart\|lat lon:30.56 N 114.46 E\|BioSampleModel:Model organism or animal	RNA seq of danio rario:adult male heart	H KO 1dpt 2	H KO 1dpt 2	normal RNA seq of Danio rerio			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505889			H-KO-1dpt-2_1.fq.gz H-KO-1dpt-2_2.fq.gz	fastq fastq	8198157000.0	27327190.0	H KO 1dpt 2 1.fq.gz	0:150 1:150	A:2235208758;C:1865834372;G:1891495548;T:2203633727;N:1984595	150	150	2235208758	1865834372	1891495548	2203633727	1984595	SRX24462836	SRS21215783	SRA1859838	Wuhan University\|Taikang Medical School (School of Basic Medical Sc	Wuhan University	2	0.9434	0.94233	0.10137	0.10074	0.71516	0.71553	0.48646	0.50212	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-06	Adult	Adult	Heart	Cardiovascular System
32016	32016	SRR28906422	SRX24462835	SRS21215784	SRP505889	PRJNA1108009	Danio rerio Raw sequence reads	PRJNA1108009	Whole Genome Sequencing	cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome				H WT UI 2		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:3mpf\|dev stage:Adult\|collection date:2023 08\|geo loc name:China:wuhan\|sex:male\|tissue:heart\|lat lon:30.56 N 114.37 E\|BioSampleModel:Model organism or animal	RNA seq of danio rario:adult male heart	H WT UI 2	H WT UI 2	normal RNA seq of Danio rerio			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505889			H-WT-UI-2_1.fq.gz H-WT-UI-2_2.fq.gz	fastq fastq	7635626400.0	25452088.0	H WT UI 2 1.fq.gz	0:150 1:150	A:2078918390;C:1742748243;G:1764521851;T:2047527957;N:1909959	150	150	2078918390	1742748243	1764521851	2047527957	1909959	SRX24462835	SRS21215784	SRA1859838	Wuhan University\|Taikang Medical School (School of Basic Medical Sc	Wuhan University	2	0.94963	0.95039	0.08529	0.08474	0.74432	0.74259	0.48965	0.49738	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-06	Adult	Adult	Heart	Cardiovascular System
32017	32017	SRR28906423	SRX24462834	SRS21215782	SRP505889	PRJNA1108009	Danio rerio Raw sequence reads	PRJNA1108009	Whole Genome Sequencing	cpt1b gene knockout KO and wild type WT zebrafish Danio Rerio cardiac transcriptome				H WT UI 1		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:3mpf\|dev stage:Adult\|collection date:2023 08\|geo loc name:China:wuhan\|sex:male\|tissue:heart\|lat lon:30.56 N 114.36 E\|BioSampleModel:Model organism or animal	RNA seq of danio rario:adult male heart	H WT UI 1	H WT UI 1	normal RNA seq of Danio rerio			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505889			H-WT-UI-1_1.fq.gz H-WT-UI-1_2.fq.gz	fastq fastq	8207182200.0	27357274.0	H WT UI 1 1.fq.gz	0:150 1:150	A:2240283347;C:1864261040;G:1888322709;T:2212265411;N:2049693	150	150	2240283347	1864261040	1888322709	2212265411	2049693	SRX24462834	SRS21215782	SRA1859838	Wuhan University\|Taikang Medical School (School of Basic Medical Sc	Wuhan University	2	0.94887	0.94936	0.08453	0.08421	0.74298	0.7428	0.50188	0.50215	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-06	Adult	Adult	Heart	Cardiovascular System
61876	61876	SRR13039579	SRX9489632	SRS7698470	SRP292270	PRJNA677856	Investigation of myocardial retionic acid signaling during heart regeneration in zebrafish	PRJNA677856	Other	Retinoic acid RA signaling is required for heart regeneration in zebrafish but the mechanism of RA mediated cardiomyocyte proliferation remains unclear. To investigate the downstream mechanism of RA mediated cardiomyocyte proliferation we generated a new transgenic line in which a loxP flanked stop cassette blocks the expression of a dominant negative form of RA receptor a b actin2:LSL dn rara and crossed this strain with a cardiomyocyte specific inducible Cre driver line cmlc2:CreER. We performed ventricular resection surgery on cmlc2:CreER; b actin2:LSL dn rara fish with and without xxx inhibition and collected 3 and 7 xxx post injury hearts to compare the gene expression profile of regenerating hearts. This project contains raw sequencing data sets of these hearts that were used to identify genes of which expression is regulated by RA signaling during regeneration.				dnRAR		strain:dnRAR\|dev stage:adult\|sex:pooled male and female\|tissue:heart\|genotype:dnRAR\|sample type:tissue sample\|BioSampleModel:Model organism or animal	dnRAR pos injury 7d prep2	dnRAR 7dpi .prep2	dnRAR pos 7dpi 2	Bulk RNA Seq polyA adult zebrafish hearts			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP292270		loader:fastq load.py	7dpi_dnrar_pos_2__Index_19__GTGAAA_L001_R1.fastq.gz 7dpi_dnrar_pos_2__Index_19__GTGAAA_L002_R1.fastq.gz	fastq fastq	2557840958.0	25325158.0	7dpi dnrar pos 2 Index 19 GTGAAA L001 R1.fastq.gz	0:101	A:696844669;C:559430636;G:554958018;T:745798221;N:809414	101		696844669	559430636	554958018	745798221	809414	SRX9489632	SRS7698470	SRA1157756	Victor Chang Cardiac Research Institute\|Genome core	Victor Chang Cardiac Research Institute	1	0.94014		0.10785		0.74742		0.51709		101		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Australia	2020-11-16	Adult	Adult	Heart	Cardiovascular System
61877	61877	SRR13039580	SRX9489631	SRS7698470	SRP292270	PRJNA677856	Investigation of myocardial retionic acid signaling during heart regeneration in zebrafish	PRJNA677856	Other	Retinoic acid RA signaling is required for heart regeneration in zebrafish but the mechanism of RA mediated cardiomyocyte proliferation remains unclear. To investigate the downstream mechanism of RA mediated cardiomyocyte proliferation we generated a new transgenic line in which a loxP flanked stop cassette blocks the expression of a dominant negative form of RA receptor a b actin2:LSL dn rara and crossed this strain with a cardiomyocyte specific inducible Cre driver line cmlc2:CreER. We performed ventricular resection surgery on cmlc2:CreER; b actin2:LSL dn rara fish with and without xxx inhibition and collected 3 and 7 xxx post injury hearts to compare the gene expression profile of regenerating hearts. This project contains raw sequencing data sets of these hearts that were used to identify genes of which expression is regulated by RA signaling during regeneration.				dnRAR		strain:dnRAR\|dev stage:adult\|sex:pooled male and female\|tissue:heart\|genotype:dnRAR\|sample type:tissue sample\|BioSampleModel:Model organism or animal	dnRAR pos injury 7d prep1	dnRAR 7dpi .prep1	dnRAR pos 7dpi 1	Bulk RNA Seq polyA adult zebrafish hearts			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP292270		loader:fastq load.py	7dpi_dnrar_pos_1__Index_7__CAGATC_L001_R1.fastq.gz 7dpi_dnrar_pos_1__Index_7__CAGATC_L002_R1.fastq.gz	fastq fastq	3132430463.0	31014163.0	7dpi dnrar pos 1 Index 7 CAGATC L001 R1.fastq.gz	0:101	A:853203437;C:688250700;G:670822036;T:919154522;N:999768	101		853203437	688250700	670822036	919154522	999768	SRX9489631	SRS7698470	SRA1157756	Victor Chang Cardiac Research Institute\|Genome core	Victor Chang Cardiac Research Institute	1	0.93753		0.11165		0.74176		0.50574		101		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Australia	2020-11-16	Adult	Adult	Heart	Cardiovascular System
61878	61878	SRR13039581	SRX9489630	SRS7698470	SRP292270	PRJNA677856	Investigation of myocardial retionic acid signaling during heart regeneration in zebrafish	PRJNA677856	Other	Retinoic acid RA signaling is required for heart regeneration in zebrafish but the mechanism of RA mediated cardiomyocyte proliferation remains unclear. To investigate the downstream mechanism of RA mediated cardiomyocyte proliferation we generated a new transgenic line in which a loxP flanked stop cassette blocks the expression of a dominant negative form of RA receptor a b actin2:LSL dn rara and crossed this strain with a cardiomyocyte specific inducible Cre driver line cmlc2:CreER. We performed ventricular resection surgery on cmlc2:CreER; b actin2:LSL dn rara fish with and without xxx inhibition and collected 3 and 7 xxx post injury hearts to compare the gene expression profile of regenerating hearts. This project contains raw sequencing data sets of these hearts that were used to identify genes of which expression is regulated by RA signaling during regeneration.				dnRAR		strain:dnRAR\|dev stage:adult\|sex:pooled male and female\|tissue:heart\|genotype:dnRAR\|sample type:tissue sample\|BioSampleModel:Model organism or animal	dnRAR neg injury 7d prep2	dnRAR 7dpi+.prep2	dnRAR neg 7dpi 2	Bulk RNA Seq polyA adult zebrafish hearts			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP292270		loader:fastq load.py	7dpi_dnrar_neg_2__Index_18__GTCCGC_L001_R1.fastq.gz 7dpi_dnrar_neg_2__Index_18__GTCCGC_L002_R1.fastq.gz	fastq fastq	2278975009.0	22564109.0	7dpi dnrar neg 2 Index 18 GTCCGC L001 R1.fastq.gz	0:101	A:635045082;C:485137051;G:490200341;T:667872440;N:720095	101		635045082	485137051	490200341	667872440	720095	SRX9489630	SRS7698470	SRA1157756	Victor Chang Cardiac Research Institute\|Genome core	Victor Chang Cardiac Research Institute	1	0.9315		0.10607		0.76242		0.51855		101		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Australia	2020-11-16	Adult	Adult	Heart	Cardiovascular System
61879	61879	SRR13039582	SRX9489629	SRS7698470	SRP292270	PRJNA677856	Investigation of myocardial retionic acid signaling during heart regeneration in zebrafish	PRJNA677856	Other	Retinoic acid RA signaling is required for heart regeneration in zebrafish but the mechanism of RA mediated cardiomyocyte proliferation remains unclear. To investigate the downstream mechanism of RA mediated cardiomyocyte proliferation we generated a new transgenic line in which a loxP flanked stop cassette blocks the expression of a dominant negative form of RA receptor a b actin2:LSL dn rara and crossed this strain with a cardiomyocyte specific inducible Cre driver line cmlc2:CreER. We performed ventricular resection surgery on cmlc2:CreER; b actin2:LSL dn rara fish with and without xxx inhibition and collected 3 and 7 xxx post injury hearts to compare the gene expression profile of regenerating hearts. This project contains raw sequencing data sets of these hearts that were used to identify genes of which expression is regulated by RA signaling during regeneration.				dnRAR		strain:dnRAR\|dev stage:adult\|sex:pooled male and female\|tissue:heart\|genotype:dnRAR\|sample type:tissue sample\|BioSampleModel:Model organism or animal	dnRAR neg injury 7d prep1	dnRAR 7dpi+.prep1	dnRAR neg 7dpi 1	Bulk RNA Seq polyA adult zebrafish hearts			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP292270		loader:fastq load.py	7dpi_dnrar_neg_1__Index_6__GCCAAT_L001_R1.fastq.gz 7dpi_dnrar_neg_1__Index_6__GCCAAT_L002_R1.fastq.gz	fastq fastq	3098671516.0	30679916.0	7dpi dnrar neg 1 Index 6 GCCAAT L001 R1.fastq.gz	0:101	A:830708694;C:679045290;G:682829533;T:905112282;N:975717	101		830708694	679045290	682829533	905112282	975717	SRX9489629	SRS7698470	SRA1157756	Victor Chang Cardiac Research Institute\|Genome core	Victor Chang Cardiac Research Institute	1	0.94733		0.08928		0.76098		0.52182		101		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Australia	2020-11-16	Adult	Adult	Heart	Cardiovascular System
61880	61880	SRR13039583	SRX9489628	SRS7698470	SRP292270	PRJNA677856	Investigation of myocardial retionic acid signaling during heart regeneration in zebrafish	PRJNA677856	Other	Retinoic acid RA signaling is required for heart regeneration in zebrafish but the mechanism of RA mediated cardiomyocyte proliferation remains unclear. To investigate the downstream mechanism of RA mediated cardiomyocyte proliferation we generated a new transgenic line in which a loxP flanked stop cassette blocks the expression of a dominant negative form of RA receptor a b actin2:LSL dn rara and crossed this strain with a cardiomyocyte specific inducible Cre driver line cmlc2:CreER. We performed ventricular resection surgery on cmlc2:CreER; b actin2:LSL dn rara fish with and without xxx inhibition and collected 3 and 7 xxx post injury hearts to compare the gene expression profile of regenerating hearts. This project contains raw sequencing data sets of these hearts that were used to identify genes of which expression is regulated by RA signaling during regeneration.				dnRAR		strain:dnRAR\|dev stage:adult\|sex:pooled male and female\|tissue:heart\|genotype:dnRAR\|sample type:tissue sample\|BioSampleModel:Model organism or animal	dnRAR pos injury 3d prep2	dnRAR 3dpi .prep2	dnRAR pos 3dpi 2	Bulk RNA Seq polyA adult zebrafish hearts			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP292270		loader:fastq load.py	3dpi_dnrar_pos_2__Index_16__CCGTCC_L001_R1.fastq.gz 3dpi_dnrar_pos_2__Index_16__CCGTCC_L002_R1.fastq.gz	fastq fastq	2552438165.0	25271665.0	3dpi dnrar pos 2 Index 16 CCGTCC L001 R1.fastq.gz	0:101	A:699918168;C:558564687;G:551754141;T:741401221;N:799948	101		699918168	558564687	551754141	741401221	799948	SRX9489628	SRS7698470	SRA1157756	Victor Chang Cardiac Research Institute\|Genome core	Victor Chang Cardiac Research Institute	1	0.93698		0.1138		0.73237		0.50509		101		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Australia	2020-11-16	Adult	Adult	Heart	Cardiovascular System
61881	61881	SRR13039584	SRX9489627	SRS7698470	SRP292270	PRJNA677856	Investigation of myocardial retionic acid signaling during heart regeneration in zebrafish	PRJNA677856	Other	Retinoic acid RA signaling is required for heart regeneration in zebrafish but the mechanism of RA mediated cardiomyocyte proliferation remains unclear. To investigate the downstream mechanism of RA mediated cardiomyocyte proliferation we generated a new transgenic line in which a loxP flanked stop cassette blocks the expression of a dominant negative form of RA receptor a b actin2:LSL dn rara and crossed this strain with a cardiomyocyte specific inducible Cre driver line cmlc2:CreER. We performed ventricular resection surgery on cmlc2:CreER; b actin2:LSL dn rara fish with and without xxx inhibition and collected 3 and 7 xxx post injury hearts to compare the gene expression profile of regenerating hearts. This project contains raw sequencing data sets of these hearts that were used to identify genes of which expression is regulated by RA signaling during regeneration.				dnRAR		strain:dnRAR\|dev stage:adult\|sex:pooled male and female\|tissue:heart\|genotype:dnRAR\|sample type:tissue sample\|BioSampleModel:Model organism or animal	dnRAR pos injury 3d prep1	dnRAR 3dpi .prep1	dnRAR pos 3dpi 1	Bulk RNA Seq polyA adult zebrafish hearts			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP292270		loader:fastq load.py	3dpi_dnrar_pos_1__Index_5__ACAGTG_L001_R1.fastq.gz 3dpi_dnrar_pos_1__Index_5__ACAGTG_L002_R1.fastq.gz	fastq fastq	2480623226.0	24560626.0	3dpi dnrar pos 1 Index 5 ACAGTG L001 R1.fastq.gz	0:101	A:671971518;C:540664685;G:537153082;T:730048562;N:785379	101		671971518	540664685	537153082	730048562	785379	SRX9489627	SRS7698470	SRA1157756	Victor Chang Cardiac Research Institute\|Genome core	Victor Chang Cardiac Research Institute	1	0.94428		0.11728		0.7427		0.49988		101		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Australia	2020-11-16	Adult	Adult	Heart	Cardiovascular System
61882	61882	SRR13039585	SRX9489626	SRS7698470	SRP292270	PRJNA677856	Investigation of myocardial retionic acid signaling during heart regeneration in zebrafish	PRJNA677856	Other	Retinoic acid RA signaling is required for heart regeneration in zebrafish but the mechanism of RA mediated cardiomyocyte proliferation remains unclear. To investigate the downstream mechanism of RA mediated cardiomyocyte proliferation we generated a new transgenic line in which a loxP flanked stop cassette blocks the expression of a dominant negative form of RA receptor a b actin2:LSL dn rara and crossed this strain with a cardiomyocyte specific inducible Cre driver line cmlc2:CreER. We performed ventricular resection surgery on cmlc2:CreER; b actin2:LSL dn rara fish with and without xxx inhibition and collected 3 and 7 xxx post injury hearts to compare the gene expression profile of regenerating hearts. This project contains raw sequencing data sets of these hearts that were used to identify genes of which expression is regulated by RA signaling during regeneration.				dnRAR		strain:dnRAR\|dev stage:adult\|sex:pooled male and female\|tissue:heart\|genotype:dnRAR\|sample type:tissue sample\|BioSampleModel:Model organism or animal	dnRAR neg injury 3d prep2	dnRAR 3dpi+.prep2	dnRAR neg 3dpi 2	Bulk RNA Seq polyA adult zebrafish hearts			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP292270		loader:fastq load.py	3dpi_dnrar_neg_2__Index_4__TGACCA_L001_R1.fastq.gz 3dpi_dnrar_neg_2__Index_4__TGACCA_L002_R1.fastq.gz	fastq fastq	3727815060.0	36909060.0	3dpi dnrar neg 2 Index 4 TGACCA L001 R1.fastq.gz	0:101	A:1007850641;C:819931567;G:814026286;T:1084822648;N:1183918	101		1007850641	819931567	814026286	1084822648	1183918	SRX9489626	SRS7698470	SRA1157756	Victor Chang Cardiac Research Institute\|Genome core	Victor Chang Cardiac Research Institute	1	0.9401		0.10133		0.73411		0.50092		101		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Australia	2020-11-16	Adult	Adult	Heart	Cardiovascular System
61883	61883	SRR13039586	SRX9489625	SRS7698470	SRP292270	PRJNA677856	Investigation of myocardial retionic acid signaling during heart regeneration in zebrafish	PRJNA677856	Other	Retinoic acid RA signaling is required for heart regeneration in zebrafish but the mechanism of RA mediated cardiomyocyte proliferation remains unclear. To investigate the downstream mechanism of RA mediated cardiomyocyte proliferation we generated a new transgenic line in which a loxP flanked stop cassette blocks the expression of a dominant negative form of RA receptor a b actin2:LSL dn rara and crossed this strain with a cardiomyocyte specific inducible Cre driver line cmlc2:CreER. We performed ventricular resection surgery on cmlc2:CreER; b actin2:LSL dn rara fish with and without xxx inhibition and collected 3 and 7 xxx post injury hearts to compare the gene expression profile of regenerating hearts. This project contains raw sequencing data sets of these hearts that were used to identify genes of which expression is regulated by RA signaling during regeneration.				dnRAR		strain:dnRAR\|dev stage:adult\|sex:pooled male and female\|tissue:heart\|genotype:dnRAR\|sample type:tissue sample\|BioSampleModel:Model organism or animal	dnRAR neg injury 3d prep1	dnRAR 3dpi+.prep1	dnRAR neg 3dpi 1	Bulk RNA Seq polyA adult zebrafish hearts			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP292270		loader:fastq load.py	3dpi_dnrar_neg_1__Index_15__ATGTCA_L001_R1.fastq.gz 3dpi_dnrar_neg_1__Index_15__ATGTCA_L002_R1.fastq.gz	fastq fastq	2223709122.0	22016922.0	3dpi dnrar neg 1 Index 15 ATGTCA L001 R1.fastq.gz	0:101	A:611860221;C:483613969;G:480670356;T:646860324;N:704252	101		611860221	483613969	480670356	646860324	704252	SRX9489625	SRS7698470	SRA1157756	Victor Chang Cardiac Research Institute\|Genome core	Victor Chang Cardiac Research Institute	1	0.93682		0.10961		0.73192		0.50015		101		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Australia	2020-11-16	Adult	Adult	Heart	Cardiovascular System
61884	61884	SRR13039587	SRX9489624	SRS7698469	SRP292270	PRJNA677856	Investigation of myocardial retionic acid signaling during heart regeneration in zebrafish	PRJNA677856	Other	Retinoic acid RA signaling is required for heart regeneration in zebrafish but the mechanism of RA mediated cardiomyocyte proliferation remains unclear. To investigate the downstream mechanism of RA mediated cardiomyocyte proliferation we generated a new transgenic line in which a loxP flanked stop cassette blocks the expression of a dominant negative form of RA receptor a b actin2:LSL dn rara and crossed this strain with a cardiomyocyte specific inducible Cre driver line cmlc2:CreER. We performed ventricular resection surgery on cmlc2:CreER; b actin2:LSL dn rara fish with and without xxx inhibition and collected 3 and 7 xxx post injury hearts to compare the gene expression profile of regenerating hearts. This project contains raw sequencing data sets of these hearts that were used to identify genes of which expression is regulated by RA signaling during regeneration.				wild type		strain:EKW\|dev stage:adult\|sex:pooled male and female\|tissue:heart\|genotype:WT\|sample type:tissue sample\|BioSampleModel:Model organism or animal	WT no injury prep2	WT 3dpi	WT no inj 2	Bulk RNA Seq polyA adult zebrafish hearts			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP292270		loader:fastq load.py	Control__Index_12__CTTGTA_L001_R1.fastq.gz Control__Index_12__CTTGTA_L002_R1.fastq.gz	fastq fastq	2875406976.0	28469376.0	Control Index 12 CTTGTA L001 R1.fastq.gz	0:101	A:775335613;C:621594724;G:635510080;T:842057810;N:908749	101		775335613	621594724	635510080	842057810	908749	SRX9489624	SRS7698469	SRA1157756	Victor Chang Cardiac Research Institute\|Genome core	Victor Chang Cardiac Research Institute	1	0.94749		0.08801		0.76824		0.46639		101		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Australia	2020-11-16	Adult	Adult	Heart	Cardiovascular System
61885	61885	SRR13039588	SRX9489623	SRS7698469	SRP292270	PRJNA677856	Investigation of myocardial retionic acid signaling during heart regeneration in zebrafish	PRJNA677856	Other	Retinoic acid RA signaling is required for heart regeneration in zebrafish but the mechanism of RA mediated cardiomyocyte proliferation remains unclear. To investigate the downstream mechanism of RA mediated cardiomyocyte proliferation we generated a new transgenic line in which a loxP flanked stop cassette blocks the expression of a dominant negative form of RA receptor a b actin2:LSL dn rara and crossed this strain with a cardiomyocyte specific inducible Cre driver line cmlc2:CreER. We performed ventricular resection surgery on cmlc2:CreER; b actin2:LSL dn rara fish with and without xxx inhibition and collected 3 and 7 xxx post injury hearts to compare the gene expression profile of regenerating hearts. This project contains raw sequencing data sets of these hearts that were used to identify genes of which expression is regulated by RA signaling during regeneration.				wild type		strain:EKW\|dev stage:adult\|sex:pooled male and female\|tissue:heart\|genotype:WT\|sample type:tissue sample\|BioSampleModel:Model organism or animal	WT no injury prep1	WT	WT no inj 1	Bulk RNA Seq polyA adult zebrafish hearts			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP292270		loader:fastq load.py	Control_1__Index_2__CGATGT_L001_R1.fastq.gz Control_1__Index_2__CGATGT_L002_R1.fastq.gz	fastq fastq	3242985366.0	32108766.0	Control 1 Index 2 CGATGT L001 R1.fastq.gz	0:101	A:855046773;C:717010168;G:731584171;T:938335515;N:1008739	101		855046773	717010168	731584171	938335515	1008739	SRX9489623	SRS7698469	SRA1157756	Victor Chang Cardiac Research Institute\|Genome core	Victor Chang Cardiac Research Institute	1	0.95209		0.07554		0.77039		0.5332		101		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Australia	2020-11-16	Adult	Adult	Heart	Cardiovascular System
63044	63044	SRR13613238	SRX10006652	SRS8175777	SRP304325	PRJNA695802	zebrafish heart RNA Sequencing	PRJNA695802	Other	To examine if the MTO1 deficiency changed the gene expression profile for thedevelopment of hypertrophic cardiomyopathy and the deficiency of complex I and IV weperformed mRNA sequencing on hearts of WT and mto1 / zebrafish at the age of 4 month 6 month.				zeMTO1 CKH		strain:zebrafish\|isolate:missing\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:6 month\|dev stage:adult\|sex:pooled male and female\|tissue:Heart\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: adult heart of wildtypeWT zebrafish	ZQH 2	ZQH 2	RNA seq libraries construction and sequencing were performed by the Novogene Bioinformatics Institute Beijing China			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP304325			M_H_WT1_1.fq.gz M_H_WT1_2.fq.gz M_H_WT2_1.fq.gz M_H_WT2_2.fq.gz M_H_WT3_1.fq.gz M_H_WT3_2.fq.gz	fastq fastq fastq fastq fastq fastq	28961958300.0	96539861.0	M H WT1 1.fq.gz	0:150 1:150	A:8024887044;C:6485327681;G:6568403520;T:7882993794;N:346261	150	150	8024887044	6485327681	6568403520	7882993794	346261	SRX10006652	SRS8175777	SRA1190610	Zhejiang University\|Institute of Genetics, Zhejiang University School	Zhejiang University	2	0.92189	0.92108	0.07211	0.07199	0.77727	0.77735	0.51037	0.51129	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-02-02	Adult	Adult	Heart	Cardiovascular System
63045	63045	SRR13613239	SRX10006651	SRS8175777	SRP304325	PRJNA695802	zebrafish heart RNA Sequencing	PRJNA695802	Other	To examine if the MTO1 deficiency changed the gene expression profile for thedevelopment of hypertrophic cardiomyopathy and the deficiency of complex I and IV weperformed mRNA sequencing on hearts of WT and mto1 / zebrafish at the age of 4 month 6 month.				zeMTO1 CKH		strain:zebrafish\|isolate:missing\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:6 month\|dev stage:adult\|sex:pooled male and female\|tissue:Heart\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: adult heart of mtu1 koMT zebrafish	ZQH 1	ZQH 1	RNA seq libraries construction and sequencing were performed by the Novogene Bioinformatics Institute Beijing China			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP304325			M_H_MT1_1.fq.gz M_H_MT1_2.fq.gz M_H_MT2_1.fq.gz M_H_MT2_2.fq.gz M_H_MT3_1.fq.gz M_H_MT3_2.fq.gz	fastq fastq fastq fastq fastq fastq	28841362200.0	96137874.0	M H MT1 1.fq.gz	0:150 1:150	A:7994584981;C:6451934158;G:6529256090;T:7865230473;N:356498	150	150	7994584981	6451934158	6529256090	7865230473	356498	SRX10006651	SRS8175777	SRA1190610	Zhejiang University\|Institute of Genetics, Zhejiang University School	Zhejiang University	2	0.93453	0.93468	0.06855	0.0684	0.77187	0.77183	0.51763	0.51889	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-02-02	Adult	Adult	Heart	Cardiovascular System
72109	72109	SRR22254566	SRX18231103	SRS15727173	SRP407212	PRJNA900016	Danio rerio Raw sequence reads	PRJNA900016	Whole Genome Sequencing	normal RNA seq of Danio rerio				WT 3		strain:AB\|dev stage:larvae\|sex:pooled male and female\|tissue:heart\|replicate:replicate = biological replicate 6\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish	WT 3	WT 3	nomal RAN Seq of zebrafish			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP407212			WT_3_1.fq.gz WT_3_2.fq.gz	fastq fastq	6636113100.0	22120377.0	WT 3 1.fq.gz	0:150 1:150	A:1848901965;C:1491873518;G:1481520683;T:1813733291;N:83643	150	150	1848901965	1491873518	1481520683	1813733291	83643	SRX18231103	SRS15727173	SRA1538502	Southwest University\|Institute of Developmental Biology and Regenerativ	Southwest University	2	0.93119	0.93088	0.10475	0.10424	0.72123	0.72111	0.46852	0.47642	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-11-10	Larval	Larval	Heart	Cardiovascular System
72110	72110	SRR22254567	SRX18231102	SRS15727172	SRP407212	PRJNA900016	Danio rerio Raw sequence reads	PRJNA900016	Whole Genome Sequencing	normal RNA seq of Danio rerio				WT 2		strain:AB\|dev stage:larvae\|sex:pooled male and female\|tissue:heart\|replicate:replicate = biological replicate 5\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish	WT 2	WT 2	nomal RAN Seq of zebrafish			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP407212			WT_2_1.fq.gz WT_2_2.fq.gz	fastq fastq	6520234800.0	21734116.0	WT 2 1.fq.gz	0:150 1:150	A:1786811917;C:1490130371;G:1488331529;T:1754878618;N:82365	150	150	1786811917	1490130371	1488331529	1754878618	82365	SRX18231102	SRS15727172	SRA1538502	Southwest University\|Institute of Developmental Biology and Regenerativ	Southwest University	2	0.93206	0.93154	0.08727	0.0867	0.72212	0.72119	0.47259	0.4715	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-11-10	Larval	Larval	Heart	Cardiovascular System
72111	72111	SRR22254568	SRX18231101	SRS15727171	SRP407212	PRJNA900016	Danio rerio Raw sequence reads	PRJNA900016	Whole Genome Sequencing	normal RNA seq of Danio rerio				WT 1		strain:AB\|dev stage:larvae\|sex:pooled male and female\|tissue:heart\|replicate:replicate = biological replicate 4\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish	WT 1	WT 1	nomal RAN Seq of zebrafish			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP407212			WT_1_1.fq.gz WT_1_2.fq.gz	fastq fastq	6598484100.0	21994947.0	WT 1 1.fq.gz	0:150 1:150	A:1808503930;C:1509705226;G:1505847513;T:1774345516;N:81915	150	150	1808503930	1509705226	1505847513	1774345516	81915	SRX18231101	SRS15727171	SRA1538502	Southwest University\|Institute of Developmental Biology and Regenerativ	Southwest University	2	0.9279	0.92749	0.0964	0.09675	0.72208	0.72297	0.47444	0.47164	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-11-10	Larval	Larval	Heart	Cardiovascular System
72112	72112	SRR22254569	SRX18231100	SRS15727170	SRP407212	PRJNA900016	Danio rerio Raw sequence reads	PRJNA900016	Whole Genome Sequencing	normal RNA seq of Danio rerio				MUT 3		strain:AB\|dev stage:larvae\|sex:pooled male and female\|tissue:heart\|replicate:replicate = biological replicate 3\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish	MUT 3	MUT 3	nomal RAN Seq of zebrafish			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP407212			Mut_3_1.fq.gz Mut_3_2.fq.gz	fastq fastq	6835792200.0	22785974.0	Mut 3 1.fq.gz	0:150 1:150	A:1897633208;C:1539576169;G:1536220827;T:1862276521;N:85475	150	150	1897633208	1539576169	1536220827	1862276521	85475	SRX18231100	SRS15727170	SRA1538502	Southwest University\|Institute of Developmental Biology and Regenerativ	Southwest University	2	0.9242	0.92324	0.10411	0.10437	0.72066	0.72062	0.47748	0.4752	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-11-10	Larval	Larval	Heart	Cardiovascular System
72113	72113	SRR22254570	SRX18231099	SRS15727169	SRP407212	PRJNA900016	Danio rerio Raw sequence reads	PRJNA900016	Whole Genome Sequencing	normal RNA seq of Danio rerio				MUT 2		strain:AB\|dev stage:larvae\|sex:pooled male and female\|tissue:heart\|replicate:replicate = biological replicate 2\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish	MUT 2	MUT 2	nomal RAN Seq of zebrafish			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP407212			Mut_2_1.fq.gz Mut_2_2.fq.gz	fastq fastq	6644473800.0	22148246.0	Mut 2 1.fq.gz	0:150 1:150	A:1849812801;C:1491771662;G:1486433132;T:1816373797;N:82408	150	150	1849812801	1491771662	1486433132	1816373797	82408	SRX18231099	SRS15727169	SRA1538502	Southwest University\|Institute of Developmental Biology and Regenerativ	Southwest University	2	0.93034	0.92955	0.09731	0.09736	0.70983	0.7108	0.4798	0.47843	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-11-10	Larval	Larval	Heart	Cardiovascular System
72114	72114	SRR22254571	SRX18231098	SRS15727168	SRP407212	PRJNA900016	Danio rerio Raw sequence reads	PRJNA900016	Whole Genome Sequencing	normal RNA seq of Danio rerio				MUT 1		strain:AB\|dev stage:larvae\|sex:pooled male and female\|tissue:heart\|replicate:replicate = biological replicate 1\|BioSampleModel:Model organism or animal	RNA Seq of zebrafish	MUT 1	MUT 1	nomal RAN Seq of zebrafish			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP407212			Mut_1_1.fq.gz Mut_1_2.fq.gz	fastq fastq	6740114700.0	22467049.0	Mut 1 1.fq.gz	0:150 1:150	A:1857778531;C:1530493212;G:1525884670;T:1825874071;N:84216	150	150	1857778531	1530493212	1525884670	1825874071	84216	SRX18231098	SRS15727168	SRA1538502	Southwest University\|Institute of Developmental Biology and Regenerativ	Southwest University	2	0.92959	0.92749	0.10647	0.10613	0.72117	0.72163	0.48318	0.47385	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-11-10	Larval	Larval	Heart	Cardiovascular System
72127	72127	SRR22258543	SRX18235012	SRS15731052	SRP407292	PRJNA900299	Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration	PRJNA900299	Other	Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.		21day post cryoinjuried	21day post cryoinjuried zebrafish heart tissues in CL	CL 21dpci 2		strain:wild type AB\|age:3 month to 1 year old\|sex:male and female\|tissue:heart\|treatment:CL\|replicate:biological replicate 2\|time point:21\|BioSampleModel:Model organism or animal	CL 21dpci replicate 2	ST19 PZ08	ST19 PZ08	CL 21day post cryoinjuried			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP407292			LTS19-PZ08_342bp_S6_L001_R1_001.fastq.gz LTS19-PZ08_342bp_S6_L001_R2_001.fastq.gz	fastq fastq	5195592665.0	18109093.0	LTS19 PZ08 342bp S6 L001 R1 001.fastq.gz	0:143.46 1:143.44	A:1373923181;C:1222085937;G:1218114278;T:1381061989;N:407280	143	143	1373923181	1222085937	1218114278	1381061989	407280	SRX18235012	SRS15731052	SRA1538914	Academia Sinica\|Institute of Biomedical Sciences	Academia Sinica	2	0.95246	0.95377	0.06297	0.06239	0.74255	0.7432	0.51136	0.5225	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Taiwan	2022-11-10	Adult	Adult	Heart	Cardiovascular System
72128	72128	SRR22258544	SRX18235011	SRS15731051	SRP407292	PRJNA900299	Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration	PRJNA900299	Other	Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.		21day post cryoinjuried	21day post cryoinjuried zebrafish heart tissues in CL	CL 21dpci 1		strain:wild type AB\|age:3 month to 1 year old\|sex:male and female\|tissue:heart\|treatment:CL\|replicate:biological replicate 1\|time point:21\|BioSampleModel:Model organism or animal	CL 21dpci replicate 1	ST19 PZ07	ST19 PZ07	CL 21day post cryoinjuried			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP407292			LTS19-PZ07_342bp_S5_L001_R1_001.fastq.gz LTS19-PZ07_342bp_S5_L001_R2_001.fastq.gz	fastq fastq	5847932195.0	20521417.0	LTS19 PZ07 342bp S5 L001 R1 001.fastq.gz	0:142.49 1:142.48	A:1557694924;C:1364216352;G:1360378421;T:1565173611;N:468887	142	142	1557694924	1364216352	1360378421	1565173611	468887	SRX18235011	SRS15731051	SRA1538914	Academia Sinica\|Institute of Biomedical Sciences	Academia Sinica	2	0.95128	0.95406	0.05502	0.05513	0.74961	0.75065	0.53433	0.52784	132	132	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Taiwan	2022-11-10	Adult	Adult	Heart	Cardiovascular System
72129	72129	SRR22258545	SRX18235010	SRS15731050	SRP407292	PRJNA900299	Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration	PRJNA900299	Other	Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.		7day post cryoinjuried	7day post cryoinjuried zebrafish heart tissues in CL	CL 7dpci 2		strain:wild type AB\|age:3 month to 1 year old\|sex:male and female\|tissue:heart\|treatment:CL\|replicate:biological replicate 2\|time point:7\|BioSampleModel:Model organism or animal	CL 7dpci replicate 2	ST19 PZ04	ST19 PZ04	CL 7day post cryoinjuried			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP407292			LTS19-PZ04_346bp_S3_L001_R1_001.fastq.gz LTS19-PZ04_346bp_S3_L001_R2_001.fastq.gz	fastq fastq	5682245028.0	19757381.0	LTS19 PZ04 346bp S3 L001 R1 001.fastq.gz	0:143.81 1:143.79	A:1506211555;C:1333061413;G:1328552313;T:1513979493;N:440254	143	143	1506211555	1333061413	1328552313	1513979493	440254	SRX18235010	SRS15731050	SRA1538914	Academia Sinica\|Institute of Biomedical Sciences	Academia Sinica	2	0.95272	0.95528	0.06697	0.06705	0.73805	0.73872	0.50736	0.50719	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Taiwan	2022-11-10	Adult	Adult	Heart	Cardiovascular System
72130	72130	SRR22258546	SRX18235009	SRS15731049	SRP407292	PRJNA900299	Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration	PRJNA900299	Other	Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.		7day post cryoinjuried	7day post cryoinjuried zebrafish heart tissues in CL	CL 7dpci 1		strain:wild type AB\|age:3 month to 1 year old\|sex:male and female\|tissue:heart\|treatment:CL\|replicate:biological replicate 1\|time point:7\|BioSampleModel:Model organism or animal	CL 7dpci replicate 1	ST19 PZ03	ST19 PZ03	CL 7day post cryoinjuried			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP407292			LTS19-PZ03_339bp_S2_L001_R1_001.fastq.gz LTS19-PZ03_339bp_S2_L001_R2_001.fastq.gz	fastq fastq	5958830725.0	20832124.0	LTS19 PZ03 339bp S2 L001 R1 001.fastq.gz	0:143.03 1:143.01	A:1576701130;C:1401162502;G:1396209763;T:1584278806;N:478524	143	143	1576701130	1401162502	1396209763	1584278806	478524	SRX18235009	SRS15731049	SRA1538914	Academia Sinica\|Institute of Biomedical Sciences	Academia Sinica	2	0.95027	0.95219	0.0614	0.06132	0.73645	0.73799	0.51433	0.51365	127	127	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Taiwan	2022-11-10	Adult	Adult	Heart	Cardiovascular System
72131	72131	SRR22258547	SRX18235008	SRS15731048	SRP407292	PRJNA900299	Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration	PRJNA900299	Other	Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.		21day post cryoinjuried	21day post cryoinjuried zebrafish heart tissues in PBS	PBS 21dpci 3		strain:wild type AB\|age:3 month to 1 year old\|sex:male and female\|tissue:heart\|treatment:PBS\|replicate:biological replicate 2\|time point:21\|BioSampleModel:Model organism or animal	PBS 21dpci replicate 2	ST19 PZ06	ST19 PZ06	PBS 21day post cryoinjuried			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP407292			LTS19-PZ06_350bp_S4_L001_R1_001.fastq.gz LTS19-PZ06_350bp_S4_L001_R2_001.fastq.gz	fastq fastq	5924347433.0	20582889.0	LTS19 PZ06 350bp S4 L001 R1 001.fastq.gz	0:143.92 1:143.90	A:1572809162;C:1387645390;G:1383614310;T:1579804471;N:474100	143	143	1572809162	1387645390	1383614310	1579804471	474100	SRX18235008	SRS15731048	SRA1538914	Academia Sinica\|Institute of Biomedical Sciences	Academia Sinica	2	0.95121	0.95404	0.05501	0.05461	0.75246	0.7528	0.5154	0.50749	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Taiwan	2022-11-10	Adult	Adult	Heart	Cardiovascular System
72132	72132	SRR22258548	SRX18235007	SRS15731047	SRP407292	PRJNA900299	Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration	PRJNA900299	Other	Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.		21day post cryoinjuried	21day post cryoinjuried zebrafish heart tissues in PBS	PBS 21dpci 1		strain:wild type AB\|age:3 month to 1 year old\|sex:male and female\|tissue:heart\|treatment:PBS\|replicate:biological replicate 1\|time point:21\|BioSampleModel:Model organism or animal	PBS 21dpci replicate 1	ST19 QF02	ST19 QF02	PBS 21day post cryoinjuried			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP407292			LTS19-QF02_340bp_S10_L001_R1_001.fastq.gz LTS19-QF02_340bp_S10_L001_R2_001.fastq.gz	fastq fastq	5232519416.0	18312949.0	LTS19 QF02 340bp S10 L001 R1 001.fastq.gz	0:142.87 1:142.86	A:1380634268;C:1233894781;G:1231023543;T:1386544969;N:421855	142	142	1380634268	1233894781	1231023543	1386544969	421855	SRX18235007	SRS15731047	SRA1538914	Academia Sinica\|Institute of Biomedical Sciences	Academia Sinica	2	0.95743	0.9589	0.05064	0.0507	0.75848	0.75962	0.50117	0.50139	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Taiwan	2022-11-10	Adult	Adult	Heart	Cardiovascular System
72133	72133	SRR22258549	SRX18235006	SRS15731046	SRP407292	PRJNA900299	Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration	PRJNA900299	Other	Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.		7day post cryoinjuried	7day post cryoinjuried zebrafish heart tissues in PBS	PBS 7dpci 3		strain:wild type AB\|age:3 month to 1 year old\|sex:male and female\|tissue:heart\|treatment:PBS\|replicate:biological replicate 2\|time point:7\|BioSampleModel:Model organism or animal	PBS 7dpci replicate 2	ST19 PZ02	ST19 PZ02	PBS 7day post cryoinjuried			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP407292			LTS19-PZ02_342bp_S1_L001_R1_001.fastq.gz LTS19-PZ02_342bp_S1_L001_R2_001.fastq.gz	fastq fastq	4506352400.0	15784899.0	LTS19 PZ02 342bp S1 L001 R1 001.fastq.gz	0:142.75 1:142.73	A:1192740332;C:1059366674;G:1055797909;T:1198088750;N:358735	142	142	1192740332	1059366674	1055797909	1198088750	358735	SRX18235006	SRS15731046	SRA1538914	Academia Sinica\|Institute of Biomedical Sciences	Academia Sinica	2	0.95404	0.9561	0.06073	0.0604	0.73996	0.74091	0.50416	0.51058	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Taiwan	2022-11-10	Adult	Adult	Heart	Cardiovascular System
72134	72134	SRR22258550	SRX18235005	SRS15731045	SRP407292	PRJNA900299	Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration	PRJNA900299	Other	Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.		7day post cryoinjuried	7day post cryoinjuried zebrafish heart tissues in PBS	PBS 7dpci 2		strain:wild type AB\|age:3 month to 1 year old\|sex:male and female\|tissue:heart\|treatment:PBS\|replicate:biological replicate 1\|time point:7\|BioSampleModel:Model organism or animal	PBS 7dpci replicate 1	ST19 QF01	ST19 QF01	PBS 7day post cryoinjuried			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP407292			LTS19-QF01_333bp_S9_L001_R1_001.fastq.gz LTS19-QF01_333bp_S9_L001_R2_001.fastq.gz	fastq fastq	4033144990.0	14237954.0	LTS19 QF01 333bp S9 L001 R1 001.fastq.gz	0:141.64 1:141.63	A:1049112811;C:966269165;G:964560615;T:1052856084;N:346315	141	141	1049112811	966269165	964560615	1052856084	346315	SRX18235005	SRS15731045	SRA1538914	Academia Sinica\|Institute of Biomedical Sciences	Academia Sinica	2	0.95546	0.95753	0.04902	0.04892	0.75112	0.75278	0.4969	0.49486	151	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Taiwan	2022-11-10	Adult	Adult	Heart	Cardiovascular System
72135	72135	SRR22258551	SRX18235004	SRS15731044	SRP407292	PRJNA900299	Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration	PRJNA900299	Other	Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.		wild type	wild type untouched zebrafish heart tissues	UT 3		strain:wild type AB\|age:3 month to 1 year old\|sex:male and female\|tissue:heart\|treatment:untouched\|replicate:biological replicate 2\|time point:0\|BioSampleModel:Model organism or animal	untouched replicate 2	LTS19 PZ10	LTS19 PZ10	untouched			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP407292			LTS19-PZ10_348bp_S8_L001_R1_001.fastq.gz LTS19-PZ10_348bp_S8_L001_R2_001.fastq.gz	fastq fastq	6431148822.0	22382395.0	LTS19 PZ10 348bp S8 L001 R1 001.fastq.gz	0:143.67 1:143.66	A:1713776212;C:1499888564;G:1494859035;T:1722122217;N:502794	143	143	1713776212	1499888564	1494859035	1722122217	502794	SRX18235004	SRS15731044	SRA1538914	Academia Sinica\|Institute of Biomedical Sciences	Academia Sinica	2	0.95513	0.95735	0.0516	0.05112	0.76514	0.76621	0.53925	0.5384	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Taiwan	2022-11-10	Adult	Adult	Heart	Cardiovascular System
72136	72136	SRR22258552	SRX18235003	SRS15731043	SRP407292	PRJNA900299	Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration	PRJNA900299	Other	Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.		wild type	wild type untouched zebrafish heart tissues	UT 2		strain:wild type AB\|age:3 month to 1 year old\|sex:male and female\|tissue:heart\|treatment:untouched\|replicate:biological replicate 1\|time point:0\|BioSampleModel:Model organism or animal	untouched replicate 1	LTS19 PZ09	LTS19 PZ09	untouched			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP407292			LTS19-PZ09_348bp_S7_L001_R1_001.fastq.gz LTS19-PZ09_348bp_S7_L001_R2_001.fastq.gz	fastq fastq	7338570795.0	25572611.0	LTS19 PZ09 348bp S7 L001 R1 001.fastq.gz	0:143.49 1:143.48	A:1951207826;C:1715917058;G:1710396299;T:1960476117;N:573495	143	143	1951207826	1715917058	1710396299	1960476117	573495	SRX18235003	SRS15731043	SRA1538914	Academia Sinica\|Institute of Biomedical Sciences	Academia Sinica	2	0.95558	0.95877	0.05288	0.05289	0.75885	0.75958	0.51637	0.51715	151	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Taiwan	2022-11-10	Adult	Adult	Heart	Cardiovascular System

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