metadata: run_metadata: 44 rows where devstage_curation_coarse = "Multi-stage" and tissue

44 rows where devstage_curation_coarse = "Multi-stage" and tissue_curation = "Heart"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
29145	29145	SRR32025076	SRX27375413	SRS23810876	SRP476805	PRJNA1050594	Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture	GSE249792	Transcriptome Analysis	Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression. In humans loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b / double knockout zebrafish larvae while smad6a / ;smad6b / double knockout zebrafish have a reduced diameter associated with early mortality. Surprisingly the smad3a / ;smad3b / ;smad6a / ;smad6b / quadruple knockout qKO zebrafish model is viable and survives to maturity although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis and that using the qKO zebrafish model thus far the only known model of aortic dissection and rupture in this species can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools each containing five smad3a / ;smad3b / ;smad6a / ;smad6b / quadruple knockout qKO zebrafish or wt control cou…			qKO 5 biol rep 1 adult aorta 3 aortas pooled	GSM8741276	source name:pool of 3 adult aortas and bulbus arteriosus\|tissue:pool of 3 adult aortas and bulbus arteriosus\|genotype:qKO\|geo loc name:missing\|collection date:missing	qKO 5 biol rep 1 adult aorta 3 aortas pooled	Raw read QC: UMI and spacer were removed using UMI tools v1.1.4 resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample trimmed reads were mapped on the zebrafish genome GRCz11 ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx	pool of 3 adult aortas and bulbus arteriosus		For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. For each sample a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.	Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf medium was refreshed. For adults zebrafish were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems Tecniplast at a constant temperature 27 28°C pH 7 5 conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.	tissue:pool of 3 adult aortas and bulbus arteriosus\|genotype:qKO	GSM8741276	GSM8741276: qKO 5 biol rep 1 adult aorta 3 aortas pooled; Danio rerio; RNA Seq	GSM8741276 r1	GSM8741276	1	For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. For each sample a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ELEMENT	Element AVITI	SRP476805		10_qKO_B9_R1.fastq.gz	fastq	1749103950.0	23321386.0	GSM8741276 r1	0:75	A:608737363;C:302455983;G:338119173;T:499492171;N:299260	75				608737363	302455983	338119173	499492171	299260	SRX27375413	SRS23810876	SRA2053000	Callewaert Lab, Biomolecular medicine, Ghent University	Callewaert Lab, Biomolecular medicine, Ghent University												B		usable mapping rate	element	element	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	Belgium	2025-01-16	Multi-stage	Multi-stage	Heart	Cardiovascular System
29146	29146	SRR32025077	SRX27375412	SRS23810877	SRP476805	PRJNA1050594	Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture	GSE249792	Transcriptome Analysis	Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression. In humans loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b / double knockout zebrafish larvae while smad6a / ;smad6b / double knockout zebrafish have a reduced diameter associated with early mortality. Surprisingly the smad3a / ;smad3b / ;smad6a / ;smad6b / quadruple knockout qKO zebrafish model is viable and survives to maturity although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis and that using the qKO zebrafish model thus far the only known model of aortic dissection and rupture in this species can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools each containing five smad3a / ;smad3b / ;smad6a / ;smad6b / quadruple knockout qKO zebrafish or wt control cou…			qKO 4 biol rep 1 adult aorta 3 aortas pooled	GSM8741275	source name:pool of 3 adult aortas and bulbus arteriosus\|tissue:pool of 3 adult aortas and bulbus arteriosus\|genotype:qKO\|geo loc name:missing\|collection date:missing	qKO 4 biol rep 1 adult aorta 3 aortas pooled	Raw read QC: UMI and spacer were removed using UMI tools v1.1.4 resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample trimmed reads were mapped on the zebrafish genome GRCz11 ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx	pool of 3 adult aortas and bulbus arteriosus		For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. For each sample a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.	Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf medium was refreshed. For adults zebrafish were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems Tecniplast at a constant temperature 27 28°C pH 7 5 conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.	tissue:pool of 3 adult aortas and bulbus arteriosus\|genotype:qKO	GSM8741275	GSM8741275: qKO 4 biol rep 1 adult aorta 3 aortas pooled; Danio rerio; RNA Seq	GSM8741275 r1	GSM8741275	1	For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. For each sample a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ELEMENT	Element AVITI	SRP476805		9_qKO_A9_R1.fastq.gz	fastq	1391151150.0	18548682.0	GSM8741275 r1	0:75	A:493715157;C:235480005;G:265878909;T:395857913;N:219166	75				493715157	235480005	265878909	395857913	219166	SRX27375412	SRS23810877	SRA2053000	Callewaert Lab, Biomolecular medicine, Ghent University	Callewaert Lab, Biomolecular medicine, Ghent University												B		usable mapping rate	element	element	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	Belgium	2025-01-16	Multi-stage	Multi-stage	Heart	Cardiovascular System
29147	29147	SRR32025078	SRX27375411	SRS23810875	SRP476805	PRJNA1050594	Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture	GSE249792	Transcriptome Analysis	Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression. In humans loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b / double knockout zebrafish larvae while smad6a / ;smad6b / double knockout zebrafish have a reduced diameter associated with early mortality. Surprisingly the smad3a / ;smad3b / ;smad6a / ;smad6b / quadruple knockout qKO zebrafish model is viable and survives to maturity although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis and that using the qKO zebrafish model thus far the only known model of aortic dissection and rupture in this species can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools each containing five smad3a / ;smad3b / ;smad6a / ;smad6b / quadruple knockout qKO zebrafish or wt control cou…			qKO 3 biol rep 1 adult aorta 3 aortas pooled	GSM8741274	source name:pool of 3 adult aortas and bulbus arteriosus\|tissue:pool of 3 adult aortas and bulbus arteriosus\|genotype:qKO\|geo loc name:missing\|collection date:missing	qKO 3 biol rep 1 adult aorta 3 aortas pooled	Raw read QC: UMI and spacer were removed using UMI tools v1.1.4 resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample trimmed reads were mapped on the zebrafish genome GRCz11 ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx	pool of 3 adult aortas and bulbus arteriosus		For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. For each sample a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.	Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf medium was refreshed. For adults zebrafish were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems Tecniplast at a constant temperature 27 28°C pH 7 5 conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.	tissue:pool of 3 adult aortas and bulbus arteriosus\|genotype:qKO	GSM8741274	GSM8741274: qKO 3 biol rep 1 adult aorta 3 aortas pooled; Danio rerio; RNA Seq	GSM8741274 r1	GSM8741274	1	For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. For each sample a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ELEMENT	Element AVITI	SRP476805		8_qKO_H8_R1.fastq.gz	fastq	1548693000.0	20649240.0	GSM8741274 r1	0:75	A:546086416;C:265907989;G:302995102;T:433434795;N:268698	75				546086416	265907989	302995102	433434795	268698	SRX27375411	SRS23810875	SRA2053000	Callewaert Lab, Biomolecular medicine, Ghent University	Callewaert Lab, Biomolecular medicine, Ghent University												B		usable mapping rate	element	element	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	Belgium	2025-01-16	Multi-stage	Multi-stage	Heart	Cardiovascular System
29148	29148	SRR32025079	SRX27375410	SRS23810873	SRP476805	PRJNA1050594	Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture	GSE249792	Transcriptome Analysis	Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression. In humans loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b / double knockout zebrafish larvae while smad6a / ;smad6b / double knockout zebrafish have a reduced diameter associated with early mortality. Surprisingly the smad3a / ;smad3b / ;smad6a / ;smad6b / quadruple knockout qKO zebrafish model is viable and survives to maturity although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis and that using the qKO zebrafish model thus far the only known model of aortic dissection and rupture in this species can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools each containing five smad3a / ;smad3b / ;smad6a / ;smad6b / quadruple knockout qKO zebrafish or wt control cou…			qKO 2 biol rep 1 adult aorta 3 aortas pooled	GSM8741273	source name:pool of 3 adult aortas and bulbus arteriosus\|tissue:pool of 3 adult aortas and bulbus arteriosus\|genotype:qKO\|geo loc name:missing\|collection date:missing	qKO 2 biol rep 1 adult aorta 3 aortas pooled	Raw read QC: UMI and spacer were removed using UMI tools v1.1.4 resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample trimmed reads were mapped on the zebrafish genome GRCz11 ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx	pool of 3 adult aortas and bulbus arteriosus		For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. For each sample a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.	Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf medium was refreshed. For adults zebrafish were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems Tecniplast at a constant temperature 27 28°C pH 7 5 conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.	tissue:pool of 3 adult aortas and bulbus arteriosus\|genotype:qKO	GSM8741273	GSM8741273: qKO 2 biol rep 1 adult aorta 3 aortas pooled; Danio rerio; RNA Seq	GSM8741273 r1	GSM8741273	1	For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. For each sample a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ELEMENT	Element AVITI	SRP476805		7_qKO_G8_R1.fastq.gz	fastq	1420837575.0	18944501.0	GSM8741273 r1	0:75	A:505066296;C:237130175;G:277345211;T:401058536;N:237357	75				505066296	237130175	277345211	401058536	237357	SRX27375410	SRS23810873	SRA2053000	Callewaert Lab, Biomolecular medicine, Ghent University	Callewaert Lab, Biomolecular medicine, Ghent University												B		usable mapping rate	element	element	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	Belgium	2025-01-16	Multi-stage	Multi-stage	Heart	Cardiovascular System
29149	29149	SRR32025080	SRX27375409	SRS23810874	SRP476805	PRJNA1050594	Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture	GSE249792	Transcriptome Analysis	Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression. In humans loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b / double knockout zebrafish larvae while smad6a / ;smad6b / double knockout zebrafish have a reduced diameter associated with early mortality. Surprisingly the smad3a / ;smad3b / ;smad6a / ;smad6b / quadruple knockout qKO zebrafish model is viable and survives to maturity although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis and that using the qKO zebrafish model thus far the only known model of aortic dissection and rupture in this species can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools each containing five smad3a / ;smad3b / ;smad6a / ;smad6b / quadruple knockout qKO zebrafish or wt control cou…			qKO 1 biol rep 1 adult aorta 3 aortas pooled	GSM8741272	source name:pool of 3 adult aortas and bulbus arteriosus\|tissue:pool of 3 adult aortas and bulbus arteriosus\|genotype:qKO\|geo loc name:missing\|collection date:missing	qKO 1 biol rep 1 adult aorta 3 aortas pooled	Raw read QC: UMI and spacer were removed using UMI tools v1.1.4 resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample trimmed reads were mapped on the zebrafish genome GRCz11 ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx	pool of 3 adult aortas and bulbus arteriosus		For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. For each sample a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.	Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf medium was refreshed. For adults zebrafish were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems Tecniplast at a constant temperature 27 28°C pH 7 5 conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.	tissue:pool of 3 adult aortas and bulbus arteriosus\|genotype:qKO	GSM8741272	GSM8741272: qKO 1 biol rep 1 adult aorta 3 aortas pooled; Danio rerio; RNA Seq	GSM8741272 r1	GSM8741272	1	For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. For each sample a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ELEMENT	Element AVITI	SRP476805		6_qKO_F8_R1.fastq.gz	fastq	1486031025.0	19813747.0	GSM8741272 r1	0:75	A:520876345;C:250796628;G:293184034;T:420907913;N:266105	75				520876345	250796628	293184034	420907913	266105	SRX27375409	SRS23810874	SRA2053000	Callewaert Lab, Biomolecular medicine, Ghent University	Callewaert Lab, Biomolecular medicine, Ghent University												B		usable mapping rate	element	element	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	Belgium	2025-01-16	Multi-stage	Multi-stage	Heart	Cardiovascular System
29150	29150	SRR32025081	SRX27375408	SRS23810872	SRP476805	PRJNA1050594	Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture	GSE249792	Transcriptome Analysis	Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression. In humans loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b / double knockout zebrafish larvae while smad6a / ;smad6b / double knockout zebrafish have a reduced diameter associated with early mortality. Surprisingly the smad3a / ;smad3b / ;smad6a / ;smad6b / quadruple knockout qKO zebrafish model is viable and survives to maturity although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis and that using the qKO zebrafish model thus far the only known model of aortic dissection and rupture in this species can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools each containing five smad3a / ;smad3b / ;smad6a / ;smad6b / quadruple knockout qKO zebrafish or wt control cou…			control 5 biol rep 1 adult aorta 3 aortas pooled	GSM8741271	source name:pool of 3 adult aortas and bulbus arteriosus\|tissue:pool of 3 adult aortas and bulbus arteriosus\|genotype:wt control\|geo loc name:missing\|collection date:missing	control 5 biol rep 1 adult aorta 3 aortas pooled	Raw read QC: UMI and spacer were removed using UMI tools v1.1.4 resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample trimmed reads were mapped on the zebrafish genome GRCz11 ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx	pool of 3 adult aortas and bulbus arteriosus		For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. For each sample a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.	Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf medium was refreshed. For adults zebrafish were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems Tecniplast at a constant temperature 27 28°C pH 7 5 conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.	tissue:pool of 3 adult aortas and bulbus arteriosus\|genotype:wt control	GSM8741271	GSM8741271: control 5 biol rep 1 adult aorta 3 aortas pooled; Danio rerio; RNA Seq	GSM8741271 r1	GSM8741271	1	For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. For each sample a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ELEMENT	Element AVITI	SRP476805		5_wt_control_E8_R1.fastq.gz	fastq	1415975175.0	18879669.0	GSM8741271 r1	0:75	A:499498659;C:237283969;G:278581269;T:400389063;N:222215	75				499498659	237283969	278581269	400389063	222215	SRX27375408	SRS23810872	SRA2053000	Callewaert Lab, Biomolecular medicine, Ghent University	Callewaert Lab, Biomolecular medicine, Ghent University												B		usable mapping rate	element	element	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	Belgium	2025-01-16	Multi-stage	Multi-stage	Heart	Cardiovascular System
29151	29151	SRR32025082	SRX27375407	SRS23810871	SRP476805	PRJNA1050594	Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture	GSE249792	Transcriptome Analysis	Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression. In humans loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b / double knockout zebrafish larvae while smad6a / ;smad6b / double knockout zebrafish have a reduced diameter associated with early mortality. Surprisingly the smad3a / ;smad3b / ;smad6a / ;smad6b / quadruple knockout qKO zebrafish model is viable and survives to maturity although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis and that using the qKO zebrafish model thus far the only known model of aortic dissection and rupture in this species can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools each containing five smad3a / ;smad3b / ;smad6a / ;smad6b / quadruple knockout qKO zebrafish or wt control cou…			control 4 biol rep 1 adult aorta 3 aortas pooled	GSM8741270	source name:pool of 3 adult aortas and bulbus arteriosus\|tissue:pool of 3 adult aortas and bulbus arteriosus\|genotype:wt control\|geo loc name:missing\|collection date:missing	control 4 biol rep 1 adult aorta 3 aortas pooled	Raw read QC: UMI and spacer were removed using UMI tools v1.1.4 resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample trimmed reads were mapped on the zebrafish genome GRCz11 ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx	pool of 3 adult aortas and bulbus arteriosus		For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. For each sample a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.	Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf medium was refreshed. For adults zebrafish were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems Tecniplast at a constant temperature 27 28°C pH 7 5 conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.	tissue:pool of 3 adult aortas and bulbus arteriosus\|genotype:wt control	GSM8741270	GSM8741270: control 4 biol rep 1 adult aorta 3 aortas pooled; Danio rerio; RNA Seq	GSM8741270 r1	GSM8741270	1	For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. For each sample a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ELEMENT	Element AVITI	SRP476805		4_wt_control_D8_R1.fastq.gz	fastq	1448565375.0	19314205.0	GSM8741270 r1	0:75	A:515361139;C:240035739;G:286658162;T:406262131;N:248204	75				515361139	240035739	286658162	406262131	248204	SRX27375407	SRS23810871	SRA2053000	Callewaert Lab, Biomolecular medicine, Ghent University	Callewaert Lab, Biomolecular medicine, Ghent University												B		usable mapping rate	element	element	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	Belgium	2025-01-16	Multi-stage	Multi-stage	Heart	Cardiovascular System
29152	29152	SRR32025083	SRX27375406	SRS23810870	SRP476805	PRJNA1050594	Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture	GSE249792	Transcriptome Analysis	Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression. In humans loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b / double knockout zebrafish larvae while smad6a / ;smad6b / double knockout zebrafish have a reduced diameter associated with early mortality. Surprisingly the smad3a / ;smad3b / ;smad6a / ;smad6b / quadruple knockout qKO zebrafish model is viable and survives to maturity although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis and that using the qKO zebrafish model thus far the only known model of aortic dissection and rupture in this species can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools each containing five smad3a / ;smad3b / ;smad6a / ;smad6b / quadruple knockout qKO zebrafish or wt control cou…			control 3 biol rep 1 adult aorta 3 aortas pooled	GSM8741269	source name:pool of 3 adult aortas and bulbus arteriosus\|tissue:pool of 3 adult aortas and bulbus arteriosus\|genotype:wt control\|geo loc name:missing\|collection date:missing	control 3 biol rep 1 adult aorta 3 aortas pooled	Raw read QC: UMI and spacer were removed using UMI tools v1.1.4 resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample trimmed reads were mapped on the zebrafish genome GRCz11 ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx	pool of 3 adult aortas and bulbus arteriosus		For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. For each sample a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.	Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf medium was refreshed. For adults zebrafish were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems Tecniplast at a constant temperature 27 28°C pH 7 5 conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.	tissue:pool of 3 adult aortas and bulbus arteriosus\|genotype:wt control	GSM8741269	GSM8741269: control 3 biol rep 1 adult aorta 3 aortas pooled; Danio rerio; RNA Seq	GSM8741269 r1	GSM8741269	1	For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. For each sample a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ELEMENT	Element AVITI	SRP476805		3_wt_control_C8_R1.fastq.gz	fastq	1171513275.0	15620177.0	GSM8741269 r1	0:75	A:417371801;C:198042286;G:227929434;T:328006138;N:163616	75				417371801	198042286	227929434	328006138	163616	SRX27375406	SRS23810870	SRA2053000	Callewaert Lab, Biomolecular medicine, Ghent University	Callewaert Lab, Biomolecular medicine, Ghent University												B		usable mapping rate	element	element	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	Belgium	2025-01-16	Multi-stage	Multi-stage	Heart	Cardiovascular System
29153	29153	SRR32025084	SRX27375405	SRS23810869	SRP476805	PRJNA1050594	Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture	GSE249792	Transcriptome Analysis	Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression. In humans loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b / double knockout zebrafish larvae while smad6a / ;smad6b / double knockout zebrafish have a reduced diameter associated with early mortality. Surprisingly the smad3a / ;smad3b / ;smad6a / ;smad6b / quadruple knockout qKO zebrafish model is viable and survives to maturity although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis and that using the qKO zebrafish model thus far the only known model of aortic dissection and rupture in this species can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools each containing five smad3a / ;smad3b / ;smad6a / ;smad6b / quadruple knockout qKO zebrafish or wt control cou…			control 2 biol rep 1 adult aorta 3 aortas pooled	GSM8741268	source name:pool of 3 adult aortas and bulbus arteriosus\|tissue:pool of 3 adult aortas and bulbus arteriosus\|genotype:wt control\|geo loc name:missing\|collection date:missing	control 2 biol rep 1 adult aorta 3 aortas pooled	Raw read QC: UMI and spacer were removed using UMI tools v1.1.4 resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample trimmed reads were mapped on the zebrafish genome GRCz11 ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx	pool of 3 adult aortas and bulbus arteriosus		For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. For each sample a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.	Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf medium was refreshed. For adults zebrafish were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems Tecniplast at a constant temperature 27 28°C pH 7 5 conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.	tissue:pool of 3 adult aortas and bulbus arteriosus\|genotype:wt control	GSM8741268	GSM8741268: control 2 biol rep 1 adult aorta 3 aortas pooled; Danio rerio; RNA Seq	GSM8741268 r1	GSM8741268	1	For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. For each sample a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ELEMENT	Element AVITI	SRP476805		2_wt_control_B8_R1.fastq.gz	fastq	1379973000.0	18399640.0	GSM8741268 r1	0:75	A:487735196;C:232122567;G:270442978;T:389464154;N:208105	75				487735196	232122567	270442978	389464154	208105	SRX27375405	SRS23810869	SRA2053000	Callewaert Lab, Biomolecular medicine, Ghent University	Callewaert Lab, Biomolecular medicine, Ghent University												B		usable mapping rate	element	element	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	Belgium	2025-01-16	Multi-stage	Multi-stage	Heart	Cardiovascular System
29154	29154	SRR32025085	SRX27375404	SRS23810868	SRP476805	PRJNA1050594	Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture	GSE249792	Transcriptome Analysis	Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression. In humans loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b / double knockout zebrafish larvae while smad6a / ;smad6b / double knockout zebrafish have a reduced diameter associated with early mortality. Surprisingly the smad3a / ;smad3b / ;smad6a / ;smad6b / quadruple knockout qKO zebrafish model is viable and survives to maturity although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis and that using the qKO zebrafish model thus far the only known model of aortic dissection and rupture in this species can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools each containing five smad3a / ;smad3b / ;smad6a / ;smad6b / quadruple knockout qKO zebrafish or wt control cou…			control 1 biol rep 1 adult aorta 3 aortas pooled	GSM8741267	source name:pool of 3 adult aortas and bulbus arteriosus\|tissue:pool of 3 adult aortas and bulbus arteriosus\|genotype:wt control\|geo loc name:missing\|collection date:missing	control 1 biol rep 1 adult aorta 3 aortas pooled	Raw read QC: UMI and spacer were removed using UMI tools v1.1.4 resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample trimmed reads were mapped on the zebrafish genome GRCz11 ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx	pool of 3 adult aortas and bulbus arteriosus		For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. For each sample a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.	Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf medium was refreshed. For adults zebrafish were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems Tecniplast at a constant temperature 27 28°C pH 7 5 conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.	tissue:pool of 3 adult aortas and bulbus arteriosus\|genotype:wt control	GSM8741267	GSM8741267: control 1 biol rep 1 adult aorta 3 aortas pooled; Danio rerio; RNA Seq	GSM8741267 r1	GSM8741267	1	For RNA extraction the Rneasy® minikit Qiagen; Hilden Germany was used following manufacturers guidelines. For each sample a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ELEMENT	Element AVITI	SRP476805		1_wt_control_A8_R1.fastq.gz	fastq	1068193125.0	14242575.0	GSM8741267 r1	0:75	A:379776425;C:179521683;G:209337737;T:299415096;N:142184	75				379776425	179521683	209337737	299415096	142184	SRX27375404	SRS23810868	SRA2053000	Callewaert Lab, Biomolecular medicine, Ghent University	Callewaert Lab, Biomolecular medicine, Ghent University												B		usable mapping rate	element	element	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	Belgium	2025-01-16	Multi-stage	Multi-stage	Heart	Cardiovascular System
52163	52163	SRR18181443	SRX14328407	SRS12144038	SRP194254	PRJNA540466	Characterization of the zebrafish cell landscape at single cell resolution	GSE130487	Transcriptome Analysis	Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.		pubmed:34660600	Heart2	GSM5924281	source name:heart\|strain:Tubingen\|tissue:heart\|genotype:wild type	Heart2	Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Mus musculus.GRCm38.88 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.	heart		Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol		strain:Tubingen\|tissue:heart\|genotype:wild type	GSM5924281	GSM5924281: Heart2; Danio rerio; RNA Seq	GSM5924281		1	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	GEO Accession:GSM5924281	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP194254	assembly:Danio rerio GRCz10\|intentional duplicate	Heart2.bam	bam	12289381500.0	40964605.0	GSM5924281 r1	0:150 1:150	A:2992562186;C:2244952830;G:2193151336;T:4856123220;N:2591928	150	150			2992562186	2244952830	2193151336	4856123220	2591928	SRX14328407	SRS12144038	SRA880843	GEO	Zhejiang University	2	0.0	0.78893	0.0	0.01228	1.0	0.91441		0.62655	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2022-03-01	Undetermined	Multi-stage	Heart	Cardiovascular System
52164	52164	SRR18181442	SRX14328406	SRS12144037	SRP194254	PRJNA540466	Characterization of the zebrafish cell landscape at single cell resolution	GSE130487	Transcriptome Analysis	Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.		pubmed:34660600	Heart1	GSM5924280	source name:heart\|strain:Tubingen\|tissue:heart\|genotype:wild type	Heart1	Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Mus musculus.GRCm38.88 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.	heart		Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol		strain:Tubingen\|tissue:heart\|genotype:wild type	GSM5924280	GSM5924280: Heart1; Danio rerio; RNA Seq	GSM5924280		1	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	GEO Accession:GSM5924280	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP194254	assembly:Danio rerio GRCz10\|intentional duplicate	Heart1.bam	bam	8428658100.0	28095527.0	GSM5924280 r1	0:150 1:150	A:2058121249;C:1561350035;G:1570099343;T:3238195048;N:892425	150	150			2058121249	1561350035	1570099343	3238195048	892425	SRX14328406	SRS12144037	SRA880843	GEO	Zhejiang University	2	2e-05	0.88435	0.0	0.01173	0.99997	0.89045	1.0	0.54187	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2022-03-01	Undetermined	Multi-stage	Heart	Cardiovascular System
52188	52188	SRR9058959	SRX5835159	SRS4761455	SRP194254	PRJNA540466	Characterization of the zebrafish cell landscape at single cell resolution	GSE130487	Transcriptome Analysis	Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.		pubmed:34660600	Heart4	GSM3768156	source name:heart\|strain:Tubingen\|genotype/variation:wild type\|tissue:heart	Heart4	Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.	heart		Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol		strain:Tubingen\|genotype/variation:wild type\|tissue:heart	GSM3768156	GSM3768156: Heart4; Danio rerio; RNA Seq	GSM3768156		1	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	GEO Accession:GSM3768156	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq X Ten	SRP194254	assembly:http://dec2017.archive.ensembl.org/Danio rerio/Info/Index	Heart4.bam	bam	52461585418.0	173713859.0	GSM3768156 r1	0:151 1:151	A:12784605546;C:9053648554;G:9236590524;T:21249234138;N:137506656	151	151			12784605546	9053648554	9236590524	21249234138	137506656	SRX5835159	SRS4761455	SRA880843	GEO	Zhejiang University	2	0.0	0.77522	0.0	0.03304	1.0	0.85632		0.55248	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2019-05-15	Undetermined	Multi-stage	Heart	Cardiovascular System
52189	52189	SRR9058958	SRX5835158	SRS4761454	SRP194254	PRJNA540466	Characterization of the zebrafish cell landscape at single cell resolution	GSE130487	Transcriptome Analysis	Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.		pubmed:34660600	Heart3	GSM3768155	source name:heart\|strain:Tubingen\|genotype/variation:wild type\|tissue:heart	Heart3	Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.	heart		Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol		strain:Tubingen\|genotype/variation:wild type\|tissue:heart	GSM3768155	GSM3768155: Heart3; Danio rerio; RNA Seq	GSM3768155		1	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	GEO Accession:GSM3768155	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq X Ten	SRP194254	assembly:http://dec2017.archive.ensembl.org/Danio rerio/Info/Index	Heart3.bam	bam	23533995978.0	77927139.0	GSM3768155 r1	0:151 1:151	A:6051087690;C:3978622675;G:3909835641;T:9588867829;N:5582143	151	151			6051087690	3978622675	3909835641	9588867829	5582143	SRX5835158	SRS4761454	SRA880843	GEO	Zhejiang University	2	0.0	0.74298	0.0	0.02452	1.0	0.88107		0.61909	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2019-05-15	Undetermined	Multi-stage	Heart	Cardiovascular System
52206	52206	SRR8991399	SRX5770467	SRS4704576	SRP194254	PRJNA540466	Characterization of the zebrafish cell landscape at single cell resolution	GSE130487	Transcriptome Analysis	Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.		pubmed:34660600	Heart5	GSM3740952	source name:heart\|strain:Tubingen\|genotype:wild type\|tissue:heart	Heart5	The drop seq core computational tool was used for preprocessing of the Microwell seq data. The implementation is described in the Drop seq computational cookbook http://mccarrolllab.org/dropseq/. Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: http://dec2017.archive.ensembl.org/Danio rerio/Info/Index Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.	heart		Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol		strain:Tubingen\|genotype:wild type\|tissue:heart	GSM3740952	GSM3740952: Heart5; Danio rerio; RNA Seq	GSM3740952		1	Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol	GEO Accession:GSM3740952	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq X Ten	SRP194254	assembly:Danio rerio GRCz10	Heart5.bam	bam	43163633400.0	143878778.0	GSM3740952 r1	0:150 1:150	A:9349719585;C:8099097553;G:8061219131;T:17651447621;N:2149510	150	150			9349719585	8099097553	8061219131	17651447621	2149510	SRX5770467	SRS4704576	SRA880843	GEO	Zhejiang University	2	0.0	0.78756	0.0	0.01363	1.0	0.8994		0.4146	150	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	microwellseq	China	2019-04-30	Undetermined	Multi-stage	Heart	Cardiovascular System
55365	55365	SRR10321288	SRX7032108	SRS5552214	SRP226527	PRJNA578764	Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.	GSE139218	Transcriptome Analysis	While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.		pubmed:31868166	FK2	GSM4134187	source name:Tgnppa:mCitrine ventricle 7dpi\|Stage:7dpi\|line:Tgnppa:mCitrine\|tissue:Adult zebrafish ventricle	FK2	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to single cells.	Tgnppa:mCitrine ventricle 7dpi	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell.	Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016		Stage:7dpi\|line:Tgnppa:mCitrine\|tissue:Adult zebrafish ventricle	GSM4134187	GSM4134187: FK2; Danio rerio; RNA Seq	GSM4134187		1	Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016	GEO Accession:GSM4134187	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP226527		Fk-2_H3MHFBGXY_S4_L001_R1_001.fastq.gz Fk-2_H3MHFBGXY_S4_L001_R2_001.fastq.gz	fastq fastq	2747645940.0	18195462.0	GSM4134187 r1	0:75.51 1:75.50	A:761850296;C:390951746;G:422952266;T:1169751842;N:2139790	75	75			761850296	390951746	422952266	1169751842	2139790	SRX7032108	SRS5552214	SRA982819	GEO	Bakkers, Hubrecht Institute	2	0.23534	0.89135	0.19366	0.15359	0.99902	0.86636	0.40119	0.71094	75	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2019-10-21	Multi-stage	Multi-stage	Heart	Cardiovascular System
55366	55366	SRR10321289	SRX7032108	SRS5552214	SRP226527	PRJNA578764	Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.	GSE139218	Transcriptome Analysis	While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.		pubmed:31868166	FK2	GSM4134187	source name:Tgnppa:mCitrine ventricle 7dpi\|Stage:7dpi\|line:Tgnppa:mCitrine\|tissue:Adult zebrafish ventricle	FK2	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to single cells.	Tgnppa:mCitrine ventricle 7dpi	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell.	Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016		Stage:7dpi\|line:Tgnppa:mCitrine\|tissue:Adult zebrafish ventricle	GSM4134187	GSM4134187: FK2; Danio rerio; RNA Seq	GSM4134187		1	Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016	GEO Accession:GSM4134187	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP226527		Fk-2_H3MHFBGXY_S4_L002_R1_001.fastq.gz Fk-2_H3MHFBGXY_S4_L002_R2_001.fastq.gz	fastq fastq	2719577388.0	18010558.0	GSM4134187 r2	0:75.50 1:75.50	A:750500832;C:383761329;G:435629268;T:1147504474;N:2181485	75	75			750500832	383761329	435629268	1147504474	2181485	SRX7032108	SRS5552214	SRA982819	GEO	Bakkers, Hubrecht Institute	2	0.21913	0.88799	0.16554	0.15559	0.99855	0.8704	0.48175	0.71083	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2019-10-21	Multi-stage	Multi-stage	Heart	Cardiovascular System
55367	55367	SRR10321290	SRX7032108	SRS5552214	SRP226527	PRJNA578764	Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.	GSE139218	Transcriptome Analysis	While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.		pubmed:31868166	FK2	GSM4134187	source name:Tgnppa:mCitrine ventricle 7dpi\|Stage:7dpi\|line:Tgnppa:mCitrine\|tissue:Adult zebrafish ventricle	FK2	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to single cells.	Tgnppa:mCitrine ventricle 7dpi	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell.	Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016		Stage:7dpi\|line:Tgnppa:mCitrine\|tissue:Adult zebrafish ventricle	GSM4134187	GSM4134187: FK2; Danio rerio; RNA Seq	GSM4134187		1	Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016	GEO Accession:GSM4134187	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP226527		Fk-2_H3MHFBGXY_S4_L003_R1_001.fastq.gz Fk-2_H3MHFBGXY_S4_L003_R2_001.fastq.gz	fastq fastq	2396848795.0	15867573.0	GSM4134187 r3	0:75.56 1:75.50	A:649358056;C:340829352;G:366620430;T:1039511314;N:529643	75	75			649358056	340829352	366620430	1039511314	529643	SRX7032108	SRS5552214	SRA982819	GEO	Bakkers, Hubrecht Institute	2	0.22581	0.89171	0.18682	0.15894	0.99928	0.87054	0.41592	0.70495	75	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2019-10-21	Multi-stage	Multi-stage	Heart	Cardiovascular System
55368	55368	SRR10321291	SRX7032108	SRS5552214	SRP226527	PRJNA578764	Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.	GSE139218	Transcriptome Analysis	While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.		pubmed:31868166	FK2	GSM4134187	source name:Tgnppa:mCitrine ventricle 7dpi\|Stage:7dpi\|line:Tgnppa:mCitrine\|tissue:Adult zebrafish ventricle	FK2	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to single cells.	Tgnppa:mCitrine ventricle 7dpi	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell.	Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016		Stage:7dpi\|line:Tgnppa:mCitrine\|tissue:Adult zebrafish ventricle	GSM4134187	GSM4134187: FK2; Danio rerio; RNA Seq	GSM4134187		1	Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016	GEO Accession:GSM4134187	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP226527		Fk-2_H3MHFBGXY_S4_L004_R1_001.fastq.gz Fk-2_H3MHFBGXY_S4_L004_R2_001.fastq.gz	fastq fastq	2610671390.0	17282452.0	GSM4134187 r4	0:75.56 1:75.50	A:691899084;C:368646569;G:415634004;T:1133907995;N:583738	75	75			691899084	368646569	415634004	1133907995	583738	SRX7032108	SRS5552214	SRA982819	GEO	Bakkers, Hubrecht Institute	2	0.24107	0.8886	0.19934	0.15491	0.99926	0.8702	0.31578	0.66998	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2019-10-21	Multi-stage	Multi-stage	Heart	Cardiovascular System
55369	55369	SRR10321284	SRX7032107	SRS5552213	SRP226527	PRJNA578764	Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.	GSE139218	Transcriptome Analysis	While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.		pubmed:31868166	FK1	GSM4134186	source name:Tgnppa:mCitrine ventricle 7dpi\|Stage:7dpi\|line:Tgnppa:mCitrine\|tissue:Adult zebrafish ventricle	FK1	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to single cells.	Tgnppa:mCitrine ventricle 7dpi	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell.	Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016		Stage:7dpi\|line:Tgnppa:mCitrine\|tissue:Adult zebrafish ventricle	GSM4134186	GSM4134186: FK1; Danio rerio; RNA Seq	GSM4134186		1	Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016	GEO Accession:GSM4134186	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP226527		FK-1_H3MHFBGXY_S3_L001_R1_001.fastq.gz FK-1_H3MHFBGXY_S3_L001_R2_001.fastq.gz	fastq fastq	2366670719.0	15672127.0	GSM4134186 r1	0:75.50 1:75.51	A:648000254;C:343663478;G:358343004;T:1014831853;N:1832130	75	75			648000254	343663478	358343004	1014831853	1832130	SRX7032107	SRS5552213	SRA982819	GEO	Bakkers, Hubrecht Institute	2	0.30353	0.90485	0.25842	0.14878	0.99912	0.85857	0.23863	0.71645	76	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2019-10-21	Multi-stage	Multi-stage	Heart	Cardiovascular System
55370	55370	SRR10321285	SRX7032107	SRS5552213	SRP226527	PRJNA578764	Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.	GSE139218	Transcriptome Analysis	While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.		pubmed:31868166	FK1	GSM4134186	source name:Tgnppa:mCitrine ventricle 7dpi\|Stage:7dpi\|line:Tgnppa:mCitrine\|tissue:Adult zebrafish ventricle	FK1	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to single cells.	Tgnppa:mCitrine ventricle 7dpi	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell.	Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016		Stage:7dpi\|line:Tgnppa:mCitrine\|tissue:Adult zebrafish ventricle	GSM4134186	GSM4134186: FK1; Danio rerio; RNA Seq	GSM4134186		1	Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016	GEO Accession:GSM4134186	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP226527		FK-1_H3MHFBGXY_S3_L002_R1_001.fastq.gz FK-1_H3MHFBGXY_S3_L002_R2_001.fastq.gz	fastq fastq	2360571906.0	15632617.0	GSM4134186 r2	0:75.49 1:75.51	A:643644738;C:339965378;G:371359828;T:1003716606;N:1885356	75	75			643644738	339965378	371359828	1003716606	1885356	SRX7032107	SRS5552213	SRA982819	GEO	Bakkers, Hubrecht Institute												T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2019-10-21	Multi-stage	Multi-stage	Heart	Cardiovascular System
55371	55371	SRR10321286	SRX7032107	SRS5552213	SRP226527	PRJNA578764	Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.	GSE139218	Transcriptome Analysis	While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.		pubmed:31868166	FK1	GSM4134186	source name:Tgnppa:mCitrine ventricle 7dpi\|Stage:7dpi\|line:Tgnppa:mCitrine\|tissue:Adult zebrafish ventricle	FK1	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to single cells.	Tgnppa:mCitrine ventricle 7dpi	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell.	Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016		Stage:7dpi\|line:Tgnppa:mCitrine\|tissue:Adult zebrafish ventricle	GSM4134186	GSM4134186: FK1; Danio rerio; RNA Seq	GSM4134186		1	Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016	GEO Accession:GSM4134186	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP226527		FK-1_H3MHFBGXY_S3_L003_R1_001.fastq.gz FK-1_H3MHFBGXY_S3_L003_R2_001.fastq.gz	fastq fastq	2074411223.0	13732357.0	GSM4134186 r3	0:75.55 1:75.51	A:554276583;C:300804770;G:312025485;T:906833457;N:470928	75	75			554276583	300804770	312025485	906833457	470928	SRX7032107	SRS5552213	SRA982819	GEO	Bakkers, Hubrecht Institute	2	0.2996	0.90397	0.25521	0.15245	0.99933	0.86314	0.21969	0.69653	75	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2019-10-21	Multi-stage	Multi-stage	Heart	Cardiovascular System
55372	55372	SRR10321287	SRX7032107	SRS5552213	SRP226527	PRJNA578764	Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.	GSE139218	Transcriptome Analysis	While the heart regenerates poorly in mammals efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone. Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity while glycolysis gene expression and glucose uptake are increased indicative for metabolic reprogramming. Mechanistically this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts. Furthermore pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine positive cells n=576 were collected from 13 cryoinjured hearts. As an internal control also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.		pubmed:31868166	FK1	GSM4134186	source name:Tgnppa:mCitrine ventricle 7dpi\|Stage:7dpi\|line:Tgnppa:mCitrine\|tissue:Adult zebrafish ventricle	FK1	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv". Read 1 was not used for quantification. Read 2 containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to single cells.	Tgnppa:mCitrine ventricle 7dpi	Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell.	Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016		Stage:7dpi\|line:Tgnppa:mCitrine\|tissue:Adult zebrafish ventricle	GSM4134186	GSM4134186: FK1; Danio rerio; RNA Seq	GSM4134186		1	Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers spike in RNA and dNTPs followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch a 4bp random molecular barcode UMI a cell specific 8bp barcode the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library the CEL seq2 protocol was used for librabry prep Hashimony et al. 2016	GEO Accession:GSM4134186	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP226527		FK-1_H3MHFBGXY_S3_L004_R1_001.fastq.gz FK-1_H3MHFBGXY_S3_L004_R2_001.fastq.gz	fastq fastq	2267459781.0	15009993.0	GSM4134186 r4	0:75.55 1:75.51	A:592957170;C:326713096;G:354670327;T:992614149;N:505039	75	75			592957170	326713096	354670327	992614149	505039	SRX7032107	SRS5552213	SRA982819	GEO	Bakkers, Hubrecht Institute	2	0.3137	0.9006	0.26295	0.14953	0.99914	0.8622	0.19895	0.70141	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	poly_a	trueseq	sc	single_cell_plate	celseq	Netherlands	2019-10-21	Multi-stage	Multi-stage	Heart	Cardiovascular System
66207	66207	SRR16097999	SRX12384068	SRS10354360	SRP339110	PRJNA767032	Amino acid primed mTOR activity is essential for heart regeneration [scRNA seq]	GSE184914	Transcriptome Analysis	Heart disease is the leading cause of death as there is no current method to repair damaged myocardium due to the limited proliferative capacity of adult cardiomyocytes. Curiously mouse neonates and zebrafish larvae or adult are able to regenerate their hearts via cardiomyocyte de differentiation and proliferation. However a molecular mechanism of why these cardiomyocytes can re enter cell cycle is poorly understood. Here we identify a unique metabolic state that primes adult zebrafish and neonatal mouse ventricular cardiomyocytes to proliferate. Zebrafish and neonatal mouse hearts display elevated glutamine levels predisposing them to amino acid driven activation of TOR. We show that this TOR activation is required for zebrafish cardiomyocyte regeneration in vivo. post injury we observe pS6 in both the epicardium and ventricular cardiomyocytes suggesting these are amino acid primed cells necessary for regeneration. Through single cell and system wide RNA sequencing LQC proteomics and microscopy we identify dramatic metabolic and mitochondrial changes during the first week of regeneration. These data suggest that regeneration of zebrafish myocardium is driven by metabolic remodeling and reveals a unique metabolic regulator TOR primed state in which zebrafish and mammalian cardiomyocytes are regeneration competent. Overall design: We performed single cell RNA seq of zebrafish heart pre injury and 3 7 xxx post injury	parent bioproject:PRJNA778001	pubmed:34988408	zebrafish day 7	GSM5600324	source name:Zebrafish heart\|tissue:heart\|strain:AB\|time:xxx post injury	zebrafish day 7	Raw reads were processed using the CellRanger software from 10X genomics using recommended default settings. Monocle version 3 alpha was used for single cell RNA seq data analysis and visualization. We kept cells with at least 200 expressed genes and 1000 Unique Molecular Identifiers UMIs and less than 40% reads mapped to mitochondrial transcripts. Genome build: GRCz10 Supplementary files format and content: tab delimited file of normalized gene level read counts for each cell	Zebrafish heart	All chemical ventricular cardiomyocyte VCM ablation were conducted on adult Zebrafish 5 mpf 12 mpf. For chemical mediated VCM ablation fish were treated with 5 mM Metronidiazole MTZ; Sigma containing 0.1% dimethyl sulfoxide DMSO or vehicle control 0.1% DMSO for 48 hours protected from light and refreshed every 24 hours. For Wnt and DKK heat shock heterozygous animals 7.5 mM MTZ was used. Following chemical treatment fish were placed back in original aquaria and hearts were collected at 0 prior to MTZ 3 7 12 and 30 xxx post injury dpi. Larval hearts 72 hpf were isolated and pooled as previously described [68 69]. 6 hearts 3 males and 3 females were isolated from Adult UI 3 dpi and 7 dpi zebrafish. Each group had 2 sets of samples of 3 hearts each for the digestion process. Each set of 3 hearts were single celled as previously described [79]. All cells per group were then pooled and sent for sequencing.	Cells were resuspended in PBS containing 0.04% BSA at a concentration of 2600 cells/ 33.8 μL solution. In total 2600 cells per sample were loaded into each well of a 10X Chromium single cell capture chip with a recovery of 272 cells for uninjured heart 141 cells for 3 xxx post injury and 368 cells for 7 xxx post injury sample. The captured cells then underwent lysis reverse transcription cDNA amplification and library preparation with indexing per the manufacturer’s protocol 10X Genomics. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc. San Diego CA using a high output 150 cycle kit with read lengths recommended by 10X Genomics.	Wild type AB; Zebrafish International Resource Center Eugene OR USA hsWnt8:GFP [Tghsp70l:Wnt8a GFPw34] and hsDKK1:GFP [Tghsp70l:DKK1b GFPw32] [19] and vmhc:mCherry NTR [Tgvmhc:mCherry Eco.NfsB] [5] were used and maintained using standard procedures [67] in accordance with the Institutional Animal Care and Use Committee approved protocols IACUC 2057 01 & 4364 02. Reverse osmosis system water is used and the water chemistry was adjusted to a temperature of 27.5°C pH of 7.5 conductivity of 800 µS hardness of 140 ppm alkalinity of 35 ppm dissolved oxygen content of 7.8 mg/L and a total gas pressure of 101%. The average nitrate level is 55 ppm the average nitrite level is 0.05 ppm and the average ammonium level is 0.01 ppm. Larval feed starting at 5 dpf dpf is a rotifer polyculture supplemented with the Zeigler larval diet at 12 dpf live artemia is added to the diet and at 60 dpf 90 dpf the fish are started on the Zeigler adult diet supplemented with live artemia once per day. The health status of the colony showed low presence of pseudoloma neurophilia and an extremely low presence of mycobacterium spp. with no major clinical or subclinical findings of significance.	tissue:heart\|strain:AB\|time:xxx post injury	GSM5600324	GSM5600324: zebrafish day 7; Danio rerio; RNA Seq	GSM5600324 r1	GSM5600324	1	Cells were resuspended in PBS containing 0.04% BSA at a concentration of 2600 cells/ 33.8 μL solution. In total 2600 cells per sample were loaded into each well of a 10X Chromium single cell capture chip with a recovery of 272 cells for uninjured heart 141 cells for 3 xxx post injury and 368 cells for 7 xxx post injury sample. The captured cells then underwent lysis reverse transcription cDNA amplification and library preparation with indexing per the manufacturer's protocol 10X Genomics. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc. San Diego CA using a high output 150 cycle kit with read lengths recommended by 10X Genomics.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP339110	assembly:GRCz10\|intentional duplicate	zf_7db_possorted_genome_bam.bam	10X Genomics bam file	38062513314.0	388392993.0	GSM5600324 r1	0:98	A:11679656809;C:7784611418;G:8037807349;T:10544896124;N:15541614	98				11679656809	7784611418	8037807349	10544896124	15541614	SRX12384068	SRS10354360	SRA1301815	Institute for Stem Cell and Regenerative Medicine	Institute for Stem Cell and Regenerative Medicine	1	0.93286		0.08896		0.87237		0.56993		98		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-28	Multi-stage	Multi-stage	Heart	Cardiovascular System
66208	66208	SRR16098000	SRX12384067	SRS10354361	SRP339110	PRJNA767032	Amino acid primed mTOR activity is essential for heart regeneration [scRNA seq]	GSE184914	Transcriptome Analysis	Heart disease is the leading cause of death as there is no current method to repair damaged myocardium due to the limited proliferative capacity of adult cardiomyocytes. Curiously mouse neonates and zebrafish larvae or adult are able to regenerate their hearts via cardiomyocyte de differentiation and proliferation. However a molecular mechanism of why these cardiomyocytes can re enter cell cycle is poorly understood. Here we identify a unique metabolic state that primes adult zebrafish and neonatal mouse ventricular cardiomyocytes to proliferate. Zebrafish and neonatal mouse hearts display elevated glutamine levels predisposing them to amino acid driven activation of TOR. We show that this TOR activation is required for zebrafish cardiomyocyte regeneration in vivo. post injury we observe pS6 in both the epicardium and ventricular cardiomyocytes suggesting these are amino acid primed cells necessary for regeneration. Through single cell and system wide RNA sequencing LQC proteomics and microscopy we identify dramatic metabolic and mitochondrial changes during the first week of regeneration. These data suggest that regeneration of zebrafish myocardium is driven by metabolic remodeling and reveals a unique metabolic regulator TOR primed state in which zebrafish and mammalian cardiomyocytes are regeneration competent. Overall design: We performed single cell RNA seq of zebrafish heart pre injury and 3 7 xxx post injury	parent bioproject:PRJNA778001	pubmed:34988408	zebrafish day 3	GSM5600323	source name:Zebrafish heart\|tissue:heart\|strain:AB\|time:xxx post injury	zebrafish day 3	Raw reads were processed using the CellRanger software from 10X genomics using recommended default settings. Monocle version 3 alpha was used for single cell RNA seq data analysis and visualization. We kept cells with at least 200 expressed genes and 1000 Unique Molecular Identifiers UMIs and less than 40% reads mapped to mitochondrial transcripts. Genome build: GRCz10 Supplementary files format and content: tab delimited file of normalized gene level read counts for each cell	Zebrafish heart	All chemical ventricular cardiomyocyte VCM ablation were conducted on adult Zebrafish 5 mpf 12 mpf. For chemical mediated VCM ablation fish were treated with 5 mM Metronidiazole MTZ; Sigma containing 0.1% dimethyl sulfoxide DMSO or vehicle control 0.1% DMSO for 48 hours protected from light and refreshed every 24 hours. For Wnt and DKK heat shock heterozygous animals 7.5 mM MTZ was used. Following chemical treatment fish were placed back in original aquaria and hearts were collected at 0 prior to MTZ 3 7 12 and 30 xxx post injury dpi. Larval hearts 72 hpf were isolated and pooled as previously described [68 69]. 6 hearts 3 males and 3 females were isolated from Adult UI 3 dpi and 7 dpi zebrafish. Each group had 2 sets of samples of 3 hearts each for the digestion process. Each set of 3 hearts were single celled as previously described [79]. All cells per group were then pooled and sent for sequencing.	Cells were resuspended in PBS containing 0.04% BSA at a concentration of 2600 cells/ 33.8 μL solution. In total 2600 cells per sample were loaded into each well of a 10X Chromium single cell capture chip with a recovery of 272 cells for uninjured heart 141 cells for 3 xxx post injury and 368 cells for 7 xxx post injury sample. The captured cells then underwent lysis reverse transcription cDNA amplification and library preparation with indexing per the manufacturer’s protocol 10X Genomics. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc. San Diego CA using a high output 150 cycle kit with read lengths recommended by 10X Genomics.	Wild type AB; Zebrafish International Resource Center Eugene OR USA hsWnt8:GFP [Tghsp70l:Wnt8a GFPw34] and hsDKK1:GFP [Tghsp70l:DKK1b GFPw32] [19] and vmhc:mCherry NTR [Tgvmhc:mCherry Eco.NfsB] [5] were used and maintained using standard procedures [67] in accordance with the Institutional Animal Care and Use Committee approved protocols IACUC 2057 01 & 4364 02. Reverse osmosis system water is used and the water chemistry was adjusted to a temperature of 27.5°C pH of 7.5 conductivity of 800 µS hardness of 140 ppm alkalinity of 35 ppm dissolved oxygen content of 7.8 mg/L and a total gas pressure of 101%. The average nitrate level is 55 ppm the average nitrite level is 0.05 ppm and the average ammonium level is 0.01 ppm. Larval feed starting at 5 dpf dpf is a rotifer polyculture supplemented with the Zeigler larval diet at 12 dpf live artemia is added to the diet and at 60 dpf 90 dpf the fish are started on the Zeigler adult diet supplemented with live artemia once per day. The health status of the colony showed low presence of pseudoloma neurophilia and an extremely low presence of mycobacterium spp. with no major clinical or subclinical findings of significance.	tissue:heart\|strain:AB\|time:xxx post injury	GSM5600323	GSM5600323: zebrafish day 3; Danio rerio; RNA Seq	GSM5600323 r1	GSM5600323	1	Cells were resuspended in PBS containing 0.04% BSA at a concentration of 2600 cells/ 33.8 μL solution. In total 2600 cells per sample were loaded into each well of a 10X Chromium single cell capture chip with a recovery of 272 cells for uninjured heart 141 cells for 3 xxx post injury and 368 cells for 7 xxx post injury sample. The captured cells then underwent lysis reverse transcription cDNA amplification and library preparation with indexing per the manufacturer's protocol 10X Genomics. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc. San Diego CA using a high output 150 cycle kit with read lengths recommended by 10X Genomics.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP339110	assembly:GRCz10\|intentional duplicate	zf_3db_possorted_genome_bam.bam	10X Genomics bam file	35567557578.0	362934261.0	GSM5600323 r1	0:98	A:11273935957;C:7072680901;G:7397087735;T:9812130858;N:11722127	98				11273935957	7072680901	7397087735	9812130858	11722127	SRX12384067	SRS10354361	SRA1301815	Institute for Stem Cell and Regenerative Medicine	Institute for Stem Cell and Regenerative Medicine	1	0.91795		0.07118		0.87418		0.58423		98		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-28	Multi-stage	Multi-stage	Heart	Cardiovascular System
66209	66209	SRR16098001	SRX12384066	SRS10354359	SRP339110	PRJNA767032	Amino acid primed mTOR activity is essential for heart regeneration [scRNA seq]	GSE184914	Transcriptome Analysis	Heart disease is the leading cause of death as there is no current method to repair damaged myocardium due to the limited proliferative capacity of adult cardiomyocytes. Curiously mouse neonates and zebrafish larvae or adult are able to regenerate their hearts via cardiomyocyte de differentiation and proliferation. However a molecular mechanism of why these cardiomyocytes can re enter cell cycle is poorly understood. Here we identify a unique metabolic state that primes adult zebrafish and neonatal mouse ventricular cardiomyocytes to proliferate. Zebrafish and neonatal mouse hearts display elevated glutamine levels predisposing them to amino acid driven activation of TOR. We show that this TOR activation is required for zebrafish cardiomyocyte regeneration in vivo. post injury we observe pS6 in both the epicardium and ventricular cardiomyocytes suggesting these are amino acid primed cells necessary for regeneration. Through single cell and system wide RNA sequencing LQC proteomics and microscopy we identify dramatic metabolic and mitochondrial changes during the first week of regeneration. These data suggest that regeneration of zebrafish myocardium is driven by metabolic remodeling and reveals a unique metabolic regulator TOR primed state in which zebrafish and mammalian cardiomyocytes are regeneration competent. Overall design: We performed single cell RNA seq of zebrafish heart pre injury and 3 7 xxx post injury	parent bioproject:PRJNA778001	pubmed:34988408	zebrafish day x	GSM5600322	source name:Zebrafish heart\|tissue:heart\|strain:AB\|time:0d	zebrafish day x	Raw reads were processed using the CellRanger software from 10X genomics using recommended default settings. Monocle version 3 alpha was used for single cell RNA seq data analysis and visualization. We kept cells with at least 200 expressed genes and 1000 Unique Molecular Identifiers UMIs and less than 40% reads mapped to mitochondrial transcripts. Genome build: GRCz10 Supplementary files format and content: tab delimited file of normalized gene level read counts for each cell	Zebrafish heart	All chemical ventricular cardiomyocyte VCM ablation were conducted on adult Zebrafish 5 mpf 12 mpf. For chemical mediated VCM ablation fish were treated with 5 mM Metronidiazole MTZ; Sigma containing 0.1% dimethyl sulfoxide DMSO or vehicle control 0.1% DMSO for 48 hours protected from light and refreshed every 24 hours. For Wnt and DKK heat shock heterozygous animals 7.5 mM MTZ was used. Following chemical treatment fish were placed back in original aquaria and hearts were collected at 0 prior to MTZ 3 7 12 and 30 xxx post injury dpi. Larval hearts 72 hpf were isolated and pooled as previously described [68 69]. 6 hearts 3 males and 3 females were isolated from Adult UI 3 dpi and 7 dpi zebrafish. Each group had 2 sets of samples of 3 hearts each for the digestion process. Each set of 3 hearts were single celled as previously described [79]. All cells per group were then pooled and sent for sequencing.	Cells were resuspended in PBS containing 0.04% BSA at a concentration of 2600 cells/ 33.8 μL solution. In total 2600 cells per sample were loaded into each well of a 10X Chromium single cell capture chip with a recovery of 272 cells for uninjured heart 141 cells for 3 xxx post injury and 368 cells for 7 xxx post injury sample. The captured cells then underwent lysis reverse transcription cDNA amplification and library preparation with indexing per the manufacturer’s protocol 10X Genomics. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc. San Diego CA using a high output 150 cycle kit with read lengths recommended by 10X Genomics.	Wild type AB; Zebrafish International Resource Center Eugene OR USA hsWnt8:GFP [Tghsp70l:Wnt8a GFPw34] and hsDKK1:GFP [Tghsp70l:DKK1b GFPw32] [19] and vmhc:mCherry NTR [Tgvmhc:mCherry Eco.NfsB] [5] were used and maintained using standard procedures [67] in accordance with the Institutional Animal Care and Use Committee approved protocols IACUC 2057 01 & 4364 02. Reverse osmosis system water is used and the water chemistry was adjusted to a temperature of 27.5°C pH of 7.5 conductivity of 800 µS hardness of 140 ppm alkalinity of 35 ppm dissolved oxygen content of 7.8 mg/L and a total gas pressure of 101%. The average nitrate level is 55 ppm the average nitrite level is 0.05 ppm and the average ammonium level is 0.01 ppm. Larval feed starting at 5 dpf dpf is a rotifer polyculture supplemented with the Zeigler larval diet at 12 dpf live artemia is added to the diet and at 60 dpf 90 dpf the fish are started on the Zeigler adult diet supplemented with live artemia once per day. The health status of the colony showed low presence of pseudoloma neurophilia and an extremely low presence of mycobacterium spp. with no major clinical or subclinical findings of significance.	tissue:heart\|strain:AB\|time:0d	GSM5600322	GSM5600322: zebrafish day x; Danio rerio; RNA Seq	GSM5600322 r1	GSM5600322	1	Cells were resuspended in PBS containing 0.04% BSA at a concentration of 2600 cells/ 33.8 μL solution. In total 2600 cells per sample were loaded into each well of a 10X Chromium single cell capture chip with a recovery of 272 cells for uninjured heart 141 cells for 3 xxx post injury and 368 cells for 7 xxx post injury sample. The captured cells then underwent lysis reverse transcription cDNA amplification and library preparation with indexing per the manufacturer's protocol 10X Genomics. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc. San Diego CA using a high output 150 cycle kit with read lengths recommended by 10X Genomics.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP339110	assembly:GRCz10\|intentional duplicate	zf_0db_possorted_genome_bam.bam	10X Genomics bam file	37627884490.0	383958005.0	GSM5600322 r1	0:98	A:12219568490;C:7567146496;G:7074688134;T:10754586205;N:11895165	98				12219568490	7567146496	7074688134	10754586205	11895165	SRX12384066	SRS10354359	SRA1301815	Institute for Stem Cell and Regenerative Medicine	Institute for Stem Cell and Regenerative Medicine	1	0.90337		0.0832		0.88562		0.62367		98		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-28	Multi-stage	Multi-stage	Heart	Cardiovascular System
66860	66860	SRR16784084	SRX12983052	SRS10923148	SRP344669	PRJNA778003	Amino acid primed mTOR activity is essential for heart regeneration [bulk RNA seq]	GSE188243	Transcriptome Analysis	Heart disease is the leading cause of death as there is no current method to repair damaged myocardium due to the limited proliferative capacity of adult cardiomyocytes. Curiously mouse neonates and zebrafish larvae or adult are able to regenerate their hearts via cardiomyocyte de differentiation and proliferation. However a molecular mechanism of why these cardiomyocytes can re enter cell cycle is poorly understood. Here we identify a unique metabolic state that primes adult zebrafish and neonatal mouse ventricular cardiomyocytes to proliferate. Zebrafish and neonatal mouse hearts display elevated glutamine levels predisposing them to amino acid driven activation of TOR. We show that this TOR activation is required for zebrafish cardiomyocyte regeneration in vivo. post injury we observe pS6 in both the epicardium and ventricular cardiomyocytes suggesting these are amino acid primed cells necessary for regeneration. Through single cell and system wide RNA sequencing LQC proteomics and microscopy we identify dramatic metabolic and mitochondrial changes during the first week of regeneration. These data suggest that regeneration of zebrafish myocardium is driven by metabolic remodeling and reveals a unique metabolic regulator TOR primed state in which zebrafish and mammalian cardiomyocytes are regeneration competent. Overall design: We performed bulk RNA seq of zebrafish heart at embryonic/fetal day 3 adult control and 3 and 7 xxx post injury.	parent bioproject:PRJNA778001	pubmed:34988408	Young day 3 heart 2	GSM5673295	source name:Zebrafish heart\|tissue:Heart\|age:Young\|treatment:N1\|time point:N1	Young day 3 heart 2	Raw reads were aligned to Ensembl GRCz10 using Tophat version 2.0.13. Gene level read counts were quantified using htseq count using Ensembl GRCz10 gene annotations. Genome build: GRCz10 Supplementary files format and content: zebrafish bulk RNAseq count matrix.txt: Tab delimited text file of counts. Supplementary files format and content: zebrafish bulk RNAseq 0 3 7 DPI reads per million.txt: Tab delimited text file of normalized gene level read counts for each cell.	Zebrafish heart	All chemical ventricular cardiomyocyte VCM ablation were conducted on adult Zebrafish 5 mpf 12 mpf. For chemical mediated VCM ablation fish were treated with 5 mM Metronidiazole MTZ; Sigma containing 0.1% dimethyl sulfoxide DMSO or vehicle control 0.1% DMSO for 48 hours protected from light and refreshed every 24 hours. For Wnt and DKK heat shock heterozygous animals 7.5 mM MTZ was used. Following chemical treatment fish were placed back in original aquaria and hearts were collected at 0 prior to MTZ 3 7 12 and 30 xxx post injury dpi. Larval hearts 72 hpf were isolated and pooled as previously described. 6 hearts 3 males and 3 females were isolated from Adult UI 3 dpi and 7 dpi zebrafish. Each group had 2 sets of samples of 3 hearts each for the digestion process. Each set of 3 hearts were single celled as previously described. All cells per group were then pooled and sent for sequencing.	For young 3 dpf zebrafish heart samples we sequenced N=2 with about n=500 hearts pooled. For the adult heart samples we sequenced N=2 hearts at UI 3 and 7 dpi with each n=4 6 pooled hearts. A negative binomial test was performed to determine significantly changed genes. Around 20 000 genes were found. RNA was isolated from young 3 dpf adult 6 mpf and regenerating 3 and 7 dpi zebrafish hearts as per manufacturers’ protocol TRIzol ThermoFisher. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc. San Diego CA.	Wild type AB; Zebrafish International Resource Center Eugene OR USA hsWnt8:GFP [Tghsp70l:Wnt8a GFPw34] and hsDKK1:GFP [Tghsp70l:DKK1b GFPw32] and vmhc:mCherry NTR [Tgvmhc:mCherry Eco.NfsB] were used and maintained using standard procedures in accordance with the Institutional Animal Care and Use Committee approved protocols IACUC 2057 01 & 4364 02. Reverse osmosis system water is used and the water chemistry was adjusted to a temperature of 27.5°C pH of 7.5 conductivity of 800 µS hardness of 140 ppm alkalinity of 35 ppm dissolved oxygen content of 7.8 mg/L and a total gas pressure of 101%. The average nitrate level is 55 ppm the average nitrite level is 0.05 ppm and the average ammonium level is 0.01 ppm. Larval feed starting at 5 dpf dpf is a rotifer polyculture supplemented with the Zeigler larval diet at 12 dpf live artemia is added to the diet and at 60 dpf 90 dpf the fish are started on the Zeigler adult diet supplemented with live artemia once per day. The health status of the colony showed low presence of pseudoloma neurophilia and an extremely low presence of mycobacterium spp. with no major clinical or subclinical findings of significance.	tissue:Heart\|age:Young\|treatment:N1\|time point:N1	GSM5673295	GSM5673295: Young day 3 heart 2; Danio rerio; RNA Seq	GSM5673295		1	For young 3 dpf zebrafish heart samples we sequenced N=2 with about n=500 hearts pooled. For the adult heart samples we sequenced N=2 hearts at UI 3 and 7 dpi with each n=4 6 pooled hearts. A negative binomial test was performed to determine significantly changed genes. Around 20 000 genes were found. RNA was isolated from young 3 dpf adult 6 mpf and regenerating 3 and 7 dpi zebrafish hearts as per manufacturers' protocol TRIzol ThermoFisher. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc. San Diego CA.	GEO Accession:GSM5673295	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP344669		AC7N1CANXX_US-1555478_CGATGT_L004_R1_001.fastq.gz AC7N1CANXX_US-1555478_CGATGT_L004_R2_001.fastq.gz	fastq fastq	2665083132.0	26128266.0	GSM5673295 r1	0:51 1:51	A:715891096;C:622224275;G:609975907;T:716605393;N:386461	51	51			715891096	622224275	609975907	716605393	386461	SRX12983052	SRS10923148	SRA1323644	GEO	Institute for Stem Cell and Regenerative Medicine	2	0.91482	0.91614	0.09011	0.091	0.70043	0.70483	0.50654	0.48799	51	51	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	United States	2021-11-04	Multi-stage	Multi-stage	Heart	Cardiovascular System
66861	66861	SRR16784083	SRX12983051	SRS10923147	SRP344669	PRJNA778003	Amino acid primed mTOR activity is essential for heart regeneration [bulk RNA seq]	GSE188243	Transcriptome Analysis	Heart disease is the leading cause of death as there is no current method to repair damaged myocardium due to the limited proliferative capacity of adult cardiomyocytes. Curiously mouse neonates and zebrafish larvae or adult are able to regenerate their hearts via cardiomyocyte de differentiation and proliferation. However a molecular mechanism of why these cardiomyocytes can re enter cell cycle is poorly understood. Here we identify a unique metabolic state that primes adult zebrafish and neonatal mouse ventricular cardiomyocytes to proliferate. Zebrafish and neonatal mouse hearts display elevated glutamine levels predisposing them to amino acid driven activation of TOR. We show that this TOR activation is required for zebrafish cardiomyocyte regeneration in vivo. post injury we observe pS6 in both the epicardium and ventricular cardiomyocytes suggesting these are amino acid primed cells necessary for regeneration. Through single cell and system wide RNA sequencing LQC proteomics and microscopy we identify dramatic metabolic and mitochondrial changes during the first week of regeneration. These data suggest that regeneration of zebrafish myocardium is driven by metabolic remodeling and reveals a unique metabolic regulator TOR primed state in which zebrafish and mammalian cardiomyocytes are regeneration competent. Overall design: We performed bulk RNA seq of zebrafish heart at embryonic/fetal day 3 adult control and 3 and 7 xxx post injury.	parent bioproject:PRJNA778001	pubmed:34988408	Young day 3 heart 1	GSM5673294	source name:Zebrafish heart\|tissue:Heart\|age:Young\|treatment:N1\|time point:N1	Young day 3 heart 1	Raw reads were aligned to Ensembl GRCz10 using Tophat version 2.0.13. Gene level read counts were quantified using htseq count using Ensembl GRCz10 gene annotations. Genome build: GRCz10 Supplementary files format and content: zebrafish bulk RNAseq count matrix.txt: Tab delimited text file of counts. Supplementary files format and content: zebrafish bulk RNAseq 0 3 7 DPI reads per million.txt: Tab delimited text file of normalized gene level read counts for each cell.	Zebrafish heart	All chemical ventricular cardiomyocyte VCM ablation were conducted on adult Zebrafish 5 mpf 12 mpf. For chemical mediated VCM ablation fish were treated with 5 mM Metronidiazole MTZ; Sigma containing 0.1% dimethyl sulfoxide DMSO or vehicle control 0.1% DMSO for 48 hours protected from light and refreshed every 24 hours. For Wnt and DKK heat shock heterozygous animals 7.5 mM MTZ was used. Following chemical treatment fish were placed back in original aquaria and hearts were collected at 0 prior to MTZ 3 7 12 and 30 xxx post injury dpi. Larval hearts 72 hpf were isolated and pooled as previously described. 6 hearts 3 males and 3 females were isolated from Adult UI 3 dpi and 7 dpi zebrafish. Each group had 2 sets of samples of 3 hearts each for the digestion process. Each set of 3 hearts were single celled as previously described. All cells per group were then pooled and sent for sequencing.	For young 3 dpf zebrafish heart samples we sequenced N=2 with about n=500 hearts pooled. For the adult heart samples we sequenced N=2 hearts at UI 3 and 7 dpi with each n=4 6 pooled hearts. A negative binomial test was performed to determine significantly changed genes. Around 20 000 genes were found. RNA was isolated from young 3 dpf adult 6 mpf and regenerating 3 and 7 dpi zebrafish hearts as per manufacturers’ protocol TRIzol ThermoFisher. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc. San Diego CA.	Wild type AB; Zebrafish International Resource Center Eugene OR USA hsWnt8:GFP [Tghsp70l:Wnt8a GFPw34] and hsDKK1:GFP [Tghsp70l:DKK1b GFPw32] and vmhc:mCherry NTR [Tgvmhc:mCherry Eco.NfsB] were used and maintained using standard procedures in accordance with the Institutional Animal Care and Use Committee approved protocols IACUC 2057 01 & 4364 02. Reverse osmosis system water is used and the water chemistry was adjusted to a temperature of 27.5°C pH of 7.5 conductivity of 800 µS hardness of 140 ppm alkalinity of 35 ppm dissolved oxygen content of 7.8 mg/L and a total gas pressure of 101%. The average nitrate level is 55 ppm the average nitrite level is 0.05 ppm and the average ammonium level is 0.01 ppm. Larval feed starting at 5 dpf dpf is a rotifer polyculture supplemented with the Zeigler larval diet at 12 dpf live artemia is added to the diet and at 60 dpf 90 dpf the fish are started on the Zeigler adult diet supplemented with live artemia once per day. The health status of the colony showed low presence of pseudoloma neurophilia and an extremely low presence of mycobacterium spp. with no major clinical or subclinical findings of significance.	tissue:Heart\|age:Young\|treatment:N1\|time point:N1	GSM5673294	GSM5673294: Young day 3 heart 1; Danio rerio; RNA Seq	GSM5673294		1	For young 3 dpf zebrafish heart samples we sequenced N=2 with about n=500 hearts pooled. For the adult heart samples we sequenced N=2 hearts at UI 3 and 7 dpi with each n=4 6 pooled hearts. A negative binomial test was performed to determine significantly changed genes. Around 20 000 genes were found. RNA was isolated from young 3 dpf adult 6 mpf and regenerating 3 and 7 dpi zebrafish hearts as per manufacturers' protocol TRIzol ThermoFisher. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc. San Diego CA.	GEO Accession:GSM5673294	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP344669		AC7N1CANXX_US-1555441_ATCACG_L004_R1_001.fastq.gz AC7N1CANXX_US-1555441_ATCACG_L004_R2_001.fastq.gz	fastq fastq	2366795862.0	23203881.0	GSM5673294 r1	0:51 1:51	A:635884570;C:553068492;G:541587629;T:635923836;N:331335	51	51			635884570	553068492	541587629	635923836	331335	SRX12983051	SRS10923147	SRA1323644	GEO	Institute for Stem Cell and Regenerative Medicine	2	0.91339	0.91347	0.08746	0.08855	0.70278	0.70822	0.49649	0.49352	51	51	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	United States	2021-11-04	Multi-stage	Multi-stage	Heart	Cardiovascular System
71060	71060	SRR21218371	SRX17229108	SRS14795574	SRP394145	PRJNA872137	The Translation Initiation Factor Homolog eif4e1c Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration.	GSE211793	Other	The?eIF4E family of translation initiation factors bind five prime methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability yet other related families exist and are all utilized in specific contexts or tissues. Here we describe a new family called Eif4e1c that is ancestral to the canonical eIF4E1A in vertebrates and for which we find roles during heart development and regeneration in zebrafish.?The Eif4e1c family is present in all aquatic vertebrates but has been lost in all terrestrial species. A core group of amino acids shared over 500 million yrs of evolution from?ray finned fish to sharks?forms an evolutionarily conserved binding interface along the surface of the protein suggesting Eif4e1c functions in a novel pathway.? Deletion of eif4e1c?in zebrafish caused growth deficits and impaired survival in juveniles.?Mutants surviving to maturity had fewer cardiomyocytes while also showing reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although?eif4e1c?is expressed in many tissues and is the predominant cap binding initiation homolog in embryos its disruption had most notable impact on the heart and at juvenile stages. ?Our findings reveal context dependent requirements for translation initiation regulators during heart regeneration. Overall design: Ribosome profiling of adult uninjured eif4e1c zebrafish mutant hearts and adult uninjured EK zebrafish wildtype hearts.		pubmed:37306388	zebrafish RNA seq Eif4e1c / rep 2 [mR2]	GSM6502520	source name:heart\|tissue:heart\|cell line:Mutant\|genotype:Eif4e1c /	zebrafish RNA seq Eif4e1c / rep 2 [mR2]	Fastq files were processed using FastQC v0.11.8; RRID:SCR 014583 for quality control QC analysis. Pre processing of sequencing reads was based on the QC report using the FASTQ Quality Filter module in the FASTX Toolkit RRID:SCR 019035. This was used to filter the bases with 99% accuracy based on Q Score. Reads were removed that showed less than 70% of nucleotides with an accuracy of at least 99%. The sequences were collapsed according to their by Unique Molecular Identifiers UMIs. Cutadapt RRID:SCR 011841 was used to trim 21 nt adaptor before the first nt and the last 4 nt from the reads to remove the UMI. The processed reads were aligned to GRCz11/danRer11 assembly of the zebrafish genome; Genome Reference Consortium using STAR v2.5.3a RRID:SCR 004463. Generated bam files were processed with RiboProfiling package v1.2.2. Coverage counts on the coding regions CDS were obtained for each sample based on RiboProfiling function modules TxDb.Drerio.UCSC.danRer11.refGene v3.4.6; Annotation package for TxDb objects; Team BC 2019 and GenomicFeatures package v1.46.1. Differential expression analysis was performed using the DESeq2 pipeline version 1.26.0 based on the expressed raw reads. Assembly: GRCz11/danRer11	heart		The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer’s instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3	Zebrafish used for ribosome profiling were grown together under normal conditions and were genotyped upon reaching maturity.	tissue:heart\|cell line:Mutant\|genotype:Eif4e1c /	GSM6502520	GSM6502520: zebrafish RNA seq Eif4e1c / rep 2 [mR2]; Danio rerio; RNA Seq	GSM6502520 r1	GSM6502520	1	The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer's instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 550	SRP394145	loader:fastq load.py	S4_mR2.fastq.gz	fastq	9679208152.0	127358002.0	GSM6502520 r1	0:76	A:2305039081;C:2189721629;G:2319593026;T:2864406960;N:447456	76				2305039081	2189721629	2319593026	2864406960	447456	SRX17229108	SRS14795574	SRA1485233	Biological Chemistry and Pharmacology, The Ohio State University	Biological Chemistry and Pharmacology, The Ohio State University	1	0.87011		0.13344		0.83633		0.75067		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-08-22	Undetermined	Multi-stage	Heart	Cardiovascular System
71061	71061	SRR21218376	SRX17229107	SRS14795573	SRP394145	PRJNA872137	The Translation Initiation Factor Homolog eif4e1c Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration.	GSE211793	Other	The?eIF4E family of translation initiation factors bind five prime methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability yet other related families exist and are all utilized in specific contexts or tissues. Here we describe a new family called Eif4e1c that is ancestral to the canonical eIF4E1A in vertebrates and for which we find roles during heart development and regeneration in zebrafish.?The Eif4e1c family is present in all aquatic vertebrates but has been lost in all terrestrial species. A core group of amino acids shared over 500 million yrs of evolution from?ray finned fish to sharks?forms an evolutionarily conserved binding interface along the surface of the protein suggesting Eif4e1c functions in a novel pathway.? Deletion of eif4e1c?in zebrafish caused growth deficits and impaired survival in juveniles.?Mutants surviving to maturity had fewer cardiomyocytes while also showing reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although?eif4e1c?is expressed in many tissues and is the predominant cap binding initiation homolog in embryos its disruption had most notable impact on the heart and at juvenile stages. ?Our findings reveal context dependent requirements for translation initiation regulators during heart regeneration. Overall design: Ribosome profiling of adult uninjured eif4e1c zebrafish mutant hearts and adult uninjured EK zebrafish wildtype hearts.		pubmed:37306388	zebrafish RNA seq Eif4e1c / rep 1 [mR1]	GSM6502519	source name:heart\|tissue:heart\|cell line:Mutant\|genotype:Eif4e1c /	zebrafish RNA seq Eif4e1c / rep 1 [mR1]	Fastq files were processed using FastQC v0.11.8; RRID:SCR 014583 for quality control QC analysis. Pre processing of sequencing reads was based on the QC report using the FASTQ Quality Filter module in the FASTX Toolkit RRID:SCR 019035. This was used to filter the bases with 99% accuracy based on Q Score. Reads were removed that showed less than 70% of nucleotides with an accuracy of at least 99%. The sequences were collapsed according to their by Unique Molecular Identifiers UMIs. Cutadapt RRID:SCR 011841 was used to trim 21 nt adaptor before the first nt and the last 4 nt from the reads to remove the UMI. The processed reads were aligned to GRCz11/danRer11 assembly of the zebrafish genome; Genome Reference Consortium using STAR v2.5.3a RRID:SCR 004463. Generated bam files were processed with RiboProfiling package v1.2.2. Coverage counts on the coding regions CDS were obtained for each sample based on RiboProfiling function modules TxDb.Drerio.UCSC.danRer11.refGene v3.4.6; Annotation package for TxDb objects; Team BC 2019 and GenomicFeatures package v1.46.1. Differential expression analysis was performed using the DESeq2 pipeline version 1.26.0 based on the expressed raw reads. Assembly: GRCz11/danRer11	heart		The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer’s instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3	Zebrafish used for ribosome profiling were grown together under normal conditions and were genotyped upon reaching maturity.	tissue:heart\|cell line:Mutant\|genotype:Eif4e1c /	GSM6502519	GSM6502519: zebrafish RNA seq Eif4e1c / rep 1 [mR1]; Danio rerio; RNA Seq	GSM6502519 r1	GSM6502519	1	The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer's instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 550	SRP394145	loader:fastq load.py	S3_mR1.fastq.gz	fastq	8635315776.0	113622576.0	GSM6502519 r1	0:76	A:2023184655;C:2026020026;G:2308108912;T:2277600404;N:401779	76				2023184655	2026020026	2308108912	2277600404	401779	SRX17229107	SRS14795573	SRA1485233	Biological Chemistry and Pharmacology, The Ohio State University	Biological Chemistry and Pharmacology, The Ohio State University	1	0.76878		0.11592		0.88154		0.77541		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-08-22	Undetermined	Multi-stage	Heart	Cardiovascular System
71062	71062	SRR21218372	SRX17229106	SRS14795572	SRP394145	PRJNA872137	The Translation Initiation Factor Homolog eif4e1c Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration.	GSE211793	Other	The?eIF4E family of translation initiation factors bind five prime methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability yet other related families exist and are all utilized in specific contexts or tissues. Here we describe a new family called Eif4e1c that is ancestral to the canonical eIF4E1A in vertebrates and for which we find roles during heart development and regeneration in zebrafish.?The Eif4e1c family is present in all aquatic vertebrates but has been lost in all terrestrial species. A core group of amino acids shared over 500 million yrs of evolution from?ray finned fish to sharks?forms an evolutionarily conserved binding interface along the surface of the protein suggesting Eif4e1c functions in a novel pathway.? Deletion of eif4e1c?in zebrafish caused growth deficits and impaired survival in juveniles.?Mutants surviving to maturity had fewer cardiomyocytes while also showing reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although?eif4e1c?is expressed in many tissues and is the predominant cap binding initiation homolog in embryos its disruption had most notable impact on the heart and at juvenile stages. ?Our findings reveal context dependent requirements for translation initiation regulators during heart regeneration. Overall design: Ribosome profiling of adult uninjured eif4e1c zebrafish mutant hearts and adult uninjured EK zebrafish wildtype hearts.		pubmed:37306388	zebrafish RNA seq Eif4e1c +/+ rep 2 [pR2]	GSM6502518	source name:heart\|tissue:heart\|cell line:Wt\|genotype:Eif4e1c +/+	zebrafish RNA seq Eif4e1c +/+ rep 2 [pR2]	Fastq files were processed using FastQC v0.11.8; RRID:SCR 014583 for quality control QC analysis. Pre processing of sequencing reads was based on the QC report using the FASTQ Quality Filter module in the FASTX Toolkit RRID:SCR 019035. This was used to filter the bases with 99% accuracy based on Q Score. Reads were removed that showed less than 70% of nucleotides with an accuracy of at least 99%. The sequences were collapsed according to their by Unique Molecular Identifiers UMIs. Cutadapt RRID:SCR 011841 was used to trim 21 nt adaptor before the first nt and the last 4 nt from the reads to remove the UMI. The processed reads were aligned to GRCz11/danRer11 assembly of the zebrafish genome; Genome Reference Consortium using STAR v2.5.3a RRID:SCR 004463. Generated bam files were processed with RiboProfiling package v1.2.2. Coverage counts on the coding regions CDS were obtained for each sample based on RiboProfiling function modules TxDb.Drerio.UCSC.danRer11.refGene v3.4.6; Annotation package for TxDb objects; Team BC 2019 and GenomicFeatures package v1.46.1. Differential expression analysis was performed using the DESeq2 pipeline version 1.26.0 based on the expressed raw reads. Assembly: GRCz11/danRer11	heart		The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer’s instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3	Zebrafish used for ribosome profiling were grown together under normal conditions and were genotyped upon reaching maturity.	tissue:heart\|cell line:Wt\|genotype:Eif4e1c +/+	GSM6502518	GSM6502518: zebrafish RNA seq Eif4e1c +/+ rep 2 [pR2]; Danio rerio; RNA Seq	GSM6502518 r1	GSM6502518	1	The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer's instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 550	SRP394145	loader:fastq load.py	S2_pR2.fastq.gz	fastq	10448850044.0	137484869.0	GSM6502518 r1	0:76	A:2430513193;C:2444194607;G:2524422424;T:3049237563;N:482257	76				2430513193	2444194607	2524422424	3049237563	482257	SRX17229106	SRS14795572	SRA1485233	Biological Chemistry and Pharmacology, The Ohio State University	Biological Chemistry and Pharmacology, The Ohio State University	1	0.8635		0.13877		0.8379		0.73623		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-08-22	Undetermined	Multi-stage	Heart	Cardiovascular System
71063	71063	SRR21218375	SRX17229105	SRS14795571	SRP394145	PRJNA872137	The Translation Initiation Factor Homolog eif4e1c Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration.	GSE211793	Other	The?eIF4E family of translation initiation factors bind five prime methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability yet other related families exist and are all utilized in specific contexts or tissues. Here we describe a new family called Eif4e1c that is ancestral to the canonical eIF4E1A in vertebrates and for which we find roles during heart development and regeneration in zebrafish.?The Eif4e1c family is present in all aquatic vertebrates but has been lost in all terrestrial species. A core group of amino acids shared over 500 million yrs of evolution from?ray finned fish to sharks?forms an evolutionarily conserved binding interface along the surface of the protein suggesting Eif4e1c functions in a novel pathway.? Deletion of eif4e1c?in zebrafish caused growth deficits and impaired survival in juveniles.?Mutants surviving to maturity had fewer cardiomyocytes while also showing reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although?eif4e1c?is expressed in many tissues and is the predominant cap binding initiation homolog in embryos its disruption had most notable impact on the heart and at juvenile stages. ?Our findings reveal context dependent requirements for translation initiation regulators during heart regeneration. Overall design: Ribosome profiling of adult uninjured eif4e1c zebrafish mutant hearts and adult uninjured EK zebrafish wildtype hearts.		pubmed:37306388	zebrafish RNA seq Eif4e1c +/+ rep 1 [pR1]	GSM6502517	source name:heart\|tissue:heart\|cell line:Wt\|genotype:Eif4e1c +/+	zebrafish RNA seq Eif4e1c +/+ rep 1 [pR1]	Fastq files were processed using FastQC v0.11.8; RRID:SCR 014583 for quality control QC analysis. Pre processing of sequencing reads was based on the QC report using the FASTQ Quality Filter module in the FASTX Toolkit RRID:SCR 019035. This was used to filter the bases with 99% accuracy based on Q Score. Reads were removed that showed less than 70% of nucleotides with an accuracy of at least 99%. The sequences were collapsed according to their by Unique Molecular Identifiers UMIs. Cutadapt RRID:SCR 011841 was used to trim 21 nt adaptor before the first nt and the last 4 nt from the reads to remove the UMI. The processed reads were aligned to GRCz11/danRer11 assembly of the zebrafish genome; Genome Reference Consortium using STAR v2.5.3a RRID:SCR 004463. Generated bam files were processed with RiboProfiling package v1.2.2. Coverage counts on the coding regions CDS were obtained for each sample based on RiboProfiling function modules TxDb.Drerio.UCSC.danRer11.refGene v3.4.6; Annotation package for TxDb objects; Team BC 2019 and GenomicFeatures package v1.46.1. Differential expression analysis was performed using the DESeq2 pipeline version 1.26.0 based on the expressed raw reads. Assembly: GRCz11/danRer11	heart		The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer’s instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3	Zebrafish used for ribosome profiling were grown together under normal conditions and were genotyped upon reaching maturity.	tissue:heart\|cell line:Wt\|genotype:Eif4e1c +/+	GSM6502517	GSM6502517: zebrafish RNA seq Eif4e1c +/+ rep 1 [pR1]; Danio rerio; RNA Seq	GSM6502517 r1	GSM6502517	1	The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer's instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 550	SRP394145	loader:fastq load.py	S1_pR1.fastq.gz	fastq	9043049240.0	118987490.0	GSM6502517 r1	0:76	A:2135845081;C:2176730805;G:2319372876;T:2410684299;N:416179	76				2135845081	2176730805	2319372876	2410684299	416179	SRX17229105	SRS14795571	SRA1485233	Biological Chemistry and Pharmacology, The Ohio State University	Biological Chemistry and Pharmacology, The Ohio State University	1	0.80924		0.17191		0.84889		0.75115		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2022-08-22	Undetermined	Multi-stage	Heart	Cardiovascular System
71064	71064	SRR21218373	SRX17229104	SRS14795570	SRP394145	PRJNA872137	The Translation Initiation Factor Homolog eif4e1c Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration.	GSE211793	Other	The?eIF4E family of translation initiation factors bind five prime methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability yet other related families exist and are all utilized in specific contexts or tissues. Here we describe a new family called Eif4e1c that is ancestral to the canonical eIF4E1A in vertebrates and for which we find roles during heart development and regeneration in zebrafish.?The Eif4e1c family is present in all aquatic vertebrates but has been lost in all terrestrial species. A core group of amino acids shared over 500 million yrs of evolution from?ray finned fish to sharks?forms an evolutionarily conserved binding interface along the surface of the protein suggesting Eif4e1c functions in a novel pathway.? Deletion of eif4e1c?in zebrafish caused growth deficits and impaired survival in juveniles.?Mutants surviving to maturity had fewer cardiomyocytes while also showing reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although?eif4e1c?is expressed in many tissues and is the predominant cap binding initiation homolog in embryos its disruption had most notable impact on the heart and at juvenile stages. ?Our findings reveal context dependent requirements for translation initiation regulators during heart regeneration. Overall design: Ribosome profiling of adult uninjured eif4e1c zebrafish mutant hearts and adult uninjured EK zebrafish wildtype hearts.		pubmed:37306388	zebrafish Ribo seq Eif4e1c / rep2 [r mR2]	GSM6502516	source name:heart\|tissue:heart\|cell line:Mutant\|genotype:Eif4e1c /	zebrafish Ribo seq Eif4e1c / rep2 [r mR2]	Fastq files were processed using FastQC v0.11.8; RRID:SCR 014583 for quality control QC analysis. Pre processing of sequencing reads was based on the QC report using the FASTQ Quality Filter module in the FASTX Toolkit RRID:SCR 019035. This was used to filter the bases with 99% accuracy based on Q Score. Reads were removed that showed less than 70% of nucleotides with an accuracy of at least 99%. The sequences were collapsed according to their by Unique Molecular Identifiers UMIs. Cutadapt RRID:SCR 011841 was used to trim 21 nt adaptor before the first nt and the last 4 nt from the reads to remove the UMI. The processed reads were aligned to GRCz11/danRer11 assembly of the zebrafish genome; Genome Reference Consortium using STAR v2.5.3a RRID:SCR 004463. Generated bam files were processed with RiboProfiling package v1.2.2. Coverage counts on the coding regions CDS were obtained for each sample based on RiboProfiling function modules TxDb.Drerio.UCSC.danRer11.refGene v3.4.6; Annotation package for TxDb objects; Team BC 2019 and GenomicFeatures package v1.46.1. Differential expression analysis was performed using the DESeq2 pipeline version 1.26.0 based on the expressed raw reads. Assembly: GRCz11/danRer11 Library strategy: Ribo seq	heart		The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer’s instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3	Zebrafish used for ribosome profiling were grown together under normal conditions and were genotyped upon reaching maturity.	tissue:heart\|cell line:Mutant\|genotype:Eif4e1c /	GSM6502516	GSM6502516: zebrafish Ribo seq Eif4e1c / rep2 [r mR2]; Danio rerio; OTHER	GSM6502516 r1	GSM6502516	1	The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer's instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3		OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 550	SRP394145		rS4_mR2.fastq.gz	fastq	6611131472.0	86988572.0	GSM6502516 r1	0:76 1:0	A:1748359123;C:1658689534;G:1706027528;T:1497702781;N:352506	76	0			1748359123	1658689534	1706027528	1497702781	352506	SRX17229104	SRS14795570	SRA1485233	Biological Chemistry and Pharmacology, The Ohio State University	Biological Chemistry and Pharmacology, The Ohio State University	1	0.0		0.0		1.0				76		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2022-08-22	Undetermined	Multi-stage	Heart	Cardiovascular System
71065	71065	SRR21218374	SRX17229103	SRS14795569	SRP394145	PRJNA872137	The Translation Initiation Factor Homolog eif4e1c Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration.	GSE211793	Other	The?eIF4E family of translation initiation factors bind five prime methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability yet other related families exist and are all utilized in specific contexts or tissues. Here we describe a new family called Eif4e1c that is ancestral to the canonical eIF4E1A in vertebrates and for which we find roles during heart development and regeneration in zebrafish.?The Eif4e1c family is present in all aquatic vertebrates but has been lost in all terrestrial species. A core group of amino acids shared over 500 million yrs of evolution from?ray finned fish to sharks?forms an evolutionarily conserved binding interface along the surface of the protein suggesting Eif4e1c functions in a novel pathway.? Deletion of eif4e1c?in zebrafish caused growth deficits and impaired survival in juveniles.?Mutants surviving to maturity had fewer cardiomyocytes while also showing reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although?eif4e1c?is expressed in many tissues and is the predominant cap binding initiation homolog in embryos its disruption had most notable impact on the heart and at juvenile stages. ?Our findings reveal context dependent requirements for translation initiation regulators during heart regeneration. Overall design: Ribosome profiling of adult uninjured eif4e1c zebrafish mutant hearts and adult uninjured EK zebrafish wildtype hearts.		pubmed:37306388	zebrafish Ribo seq Eif4e1c / rep 1 [r mR1]	GSM6502515	source name:heart\|tissue:heart\|cell line:Mutant\|genotype:Eif4e1c /	zebrafish Ribo seq Eif4e1c / rep 1 [r mR1]	Fastq files were processed using FastQC v0.11.8; RRID:SCR 014583 for quality control QC analysis. Pre processing of sequencing reads was based on the QC report using the FASTQ Quality Filter module in the FASTX Toolkit RRID:SCR 019035. This was used to filter the bases with 99% accuracy based on Q Score. Reads were removed that showed less than 70% of nucleotides with an accuracy of at least 99%. The sequences were collapsed according to their by Unique Molecular Identifiers UMIs. Cutadapt RRID:SCR 011841 was used to trim 21 nt adaptor before the first nt and the last 4 nt from the reads to remove the UMI. The processed reads were aligned to GRCz11/danRer11 assembly of the zebrafish genome; Genome Reference Consortium using STAR v2.5.3a RRID:SCR 004463. Generated bam files were processed with RiboProfiling package v1.2.2. Coverage counts on the coding regions CDS were obtained for each sample based on RiboProfiling function modules TxDb.Drerio.UCSC.danRer11.refGene v3.4.6; Annotation package for TxDb objects; Team BC 2019 and GenomicFeatures package v1.46.1. Differential expression analysis was performed using the DESeq2 pipeline version 1.26.0 based on the expressed raw reads. Assembly: GRCz11/danRer11 Library strategy: Ribo seq	heart		The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer’s instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3	Zebrafish used for ribosome profiling were grown together under normal conditions and were genotyped upon reaching maturity.	tissue:heart\|cell line:Mutant\|genotype:Eif4e1c /	GSM6502515	GSM6502515: zebrafish Ribo seq Eif4e1c / rep 1 [r mR1]; Danio rerio; OTHER	GSM6502515 r1	GSM6502515	1	The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer's instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3		OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 550	SRP394145		rS3_mR1.fastq.gz	fastq	13677356644.0	179965219.0	GSM6502515 r1	0:76 1:0	A:3346749848;C:3412648254;G:3629003006;T:3288222747;N:732789	76	0			3346749848	3412648254	3629003006	3288222747	732789	SRX17229103	SRS14795569	SRA1485233	Biological Chemistry and Pharmacology, The Ohio State University	Biological Chemistry and Pharmacology, The Ohio State University	1	0.0		0.0		1.0				76		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2022-08-22	Undetermined	Multi-stage	Heart	Cardiovascular System
71066	71066	SRR21218377	SRX17229102	SRS14795568	SRP394145	PRJNA872137	The Translation Initiation Factor Homolog eif4e1c Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration.	GSE211793	Other	The?eIF4E family of translation initiation factors bind five prime methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability yet other related families exist and are all utilized in specific contexts or tissues. Here we describe a new family called Eif4e1c that is ancestral to the canonical eIF4E1A in vertebrates and for which we find roles during heart development and regeneration in zebrafish.?The Eif4e1c family is present in all aquatic vertebrates but has been lost in all terrestrial species. A core group of amino acids shared over 500 million yrs of evolution from?ray finned fish to sharks?forms an evolutionarily conserved binding interface along the surface of the protein suggesting Eif4e1c functions in a novel pathway.? Deletion of eif4e1c?in zebrafish caused growth deficits and impaired survival in juveniles.?Mutants surviving to maturity had fewer cardiomyocytes while also showing reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although?eif4e1c?is expressed in many tissues and is the predominant cap binding initiation homolog in embryos its disruption had most notable impact on the heart and at juvenile stages. ?Our findings reveal context dependent requirements for translation initiation regulators during heart regeneration. Overall design: Ribosome profiling of adult uninjured eif4e1c zebrafish mutant hearts and adult uninjured EK zebrafish wildtype hearts.		pubmed:37306388	zebrafish Ribo seq Eif4e1c +/+ rep 2 [r pR2]	GSM6502514	source name:heart\|tissue:heart\|cell line:Wt\|genotype:Eif4e1c +/+	zebrafish Ribo seq Eif4e1c +/+ rep 2 [r pR2]	Fastq files were processed using FastQC v0.11.8; RRID:SCR 014583 for quality control QC analysis. Pre processing of sequencing reads was based on the QC report using the FASTQ Quality Filter module in the FASTX Toolkit RRID:SCR 019035. This was used to filter the bases with 99% accuracy based on Q Score. Reads were removed that showed less than 70% of nucleotides with an accuracy of at least 99%. The sequences were collapsed according to their by Unique Molecular Identifiers UMIs. Cutadapt RRID:SCR 011841 was used to trim 21 nt adaptor before the first nt and the last 4 nt from the reads to remove the UMI. The processed reads were aligned to GRCz11/danRer11 assembly of the zebrafish genome; Genome Reference Consortium using STAR v2.5.3a RRID:SCR 004463. Generated bam files were processed with RiboProfiling package v1.2.2. Coverage counts on the coding regions CDS were obtained for each sample based on RiboProfiling function modules TxDb.Drerio.UCSC.danRer11.refGene v3.4.6; Annotation package for TxDb objects; Team BC 2019 and GenomicFeatures package v1.46.1. Differential expression analysis was performed using the DESeq2 pipeline version 1.26.0 based on the expressed raw reads. Assembly: GRCz11/danRer11 Library strategy: Ribo seq	heart		The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer’s instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3	Zebrafish used for ribosome profiling were grown together under normal conditions and were genotyped upon reaching maturity.	tissue:heart\|cell line:Wt\|genotype:Eif4e1c +/+	GSM6502514	GSM6502514: zebrafish Ribo seq Eif4e1c +/+ rep 2 [r pR2]; Danio rerio; OTHER	GSM6502514 r1	GSM6502514	1	The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer's instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3		OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 550	SRP394145		rS2_pR2.fastq.gz	fastq	8919983048.0	117368198.0	GSM6502514 r1	0:76 1:0	A:2208663451;C:2257902067;G:2371468879;T:2081476473;N:472178	76	0			2208663451	2257902067	2371468879	2081476473	472178	SRX17229102	SRS14795568	SRA1485233	Biological Chemistry and Pharmacology, The Ohio State University	Biological Chemistry and Pharmacology, The Ohio State University	1	1e-05		0.0		0.99997		1.0		76		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2022-08-22	Undetermined	Multi-stage	Heart	Cardiovascular System
71067	71067	SRR21218378	SRX17229101	SRS14795567	SRP394145	PRJNA872137	The Translation Initiation Factor Homolog eif4e1c Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration.	GSE211793	Other	The?eIF4E family of translation initiation factors bind five prime methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability yet other related families exist and are all utilized in specific contexts or tissues. Here we describe a new family called Eif4e1c that is ancestral to the canonical eIF4E1A in vertebrates and for which we find roles during heart development and regeneration in zebrafish.?The Eif4e1c family is present in all aquatic vertebrates but has been lost in all terrestrial species. A core group of amino acids shared over 500 million yrs of evolution from?ray finned fish to sharks?forms an evolutionarily conserved binding interface along the surface of the protein suggesting Eif4e1c functions in a novel pathway.? Deletion of eif4e1c?in zebrafish caused growth deficits and impaired survival in juveniles.?Mutants surviving to maturity had fewer cardiomyocytes while also showing reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although?eif4e1c?is expressed in many tissues and is the predominant cap binding initiation homolog in embryos its disruption had most notable impact on the heart and at juvenile stages. ?Our findings reveal context dependent requirements for translation initiation regulators during heart regeneration. Overall design: Ribosome profiling of adult uninjured eif4e1c zebrafish mutant hearts and adult uninjured EK zebrafish wildtype hearts.		pubmed:37306388	zebrafish Ribo seq Eif4e1c +/+ rep 1 [r pR1]	GSM6502513	source name:heart\|tissue:heart\|cell line:Wt\|genotype:Eif4e1c +/+	zebrafish Ribo seq Eif4e1c +/+ rep 1 [r pR1]	Fastq files were processed using FastQC v0.11.8; RRID:SCR 014583 for quality control QC analysis. Pre processing of sequencing reads was based on the QC report using the FASTQ Quality Filter module in the FASTX Toolkit RRID:SCR 019035. This was used to filter the bases with 99% accuracy based on Q Score. Reads were removed that showed less than 70% of nucleotides with an accuracy of at least 99%. The sequences were collapsed according to their by Unique Molecular Identifiers UMIs. Cutadapt RRID:SCR 011841 was used to trim 21 nt adaptor before the first nt and the last 4 nt from the reads to remove the UMI. The processed reads were aligned to GRCz11/danRer11 assembly of the zebrafish genome; Genome Reference Consortium using STAR v2.5.3a RRID:SCR 004463. Generated bam files were processed with RiboProfiling package v1.2.2. Coverage counts on the coding regions CDS were obtained for each sample based on RiboProfiling function modules TxDb.Drerio.UCSC.danRer11.refGene v3.4.6; Annotation package for TxDb objects; Team BC 2019 and GenomicFeatures package v1.46.1. Differential expression analysis was performed using the DESeq2 pipeline version 1.26.0 based on the expressed raw reads. Assembly: GRCz11/danRer11 Library strategy: Ribo seq	heart		The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer’s instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3	Zebrafish used for ribosome profiling were grown together under normal conditions and were genotyped upon reaching maturity.	tissue:heart\|cell line:Wt\|genotype:Eif4e1c +/+	GSM6502513	GSM6502513: zebrafish Ribo seq Eif4e1c +/+ rep 1 [r pR1]; Danio rerio; OTHER	GSM6502513 r1	GSM6502513	1	The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB CaCl2 5mM final concentration and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer's instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at 20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3		OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	NextSeq 550	SRP394145		rS1_pR1.fastq.gz	fastq	8551941876.0	112525551.0	GSM6502513 r1	0:76 1:0	A:2015417703;C:2191682962;G:2364697448;T:1979683824;N:459939	76	0			2015417703	2191682962	2364697448	1979683824	459939	SRX17229101	SRS14795567	SRA1485233	Biological Chemistry and Pharmacology, The Ohio State University	Biological Chemistry and Pharmacology, The Ohio State University	1	1e-05		0.0		0.99997		0.0		76		T		under 1.2% mapping rate	illumina	nextseq	unknown	other	unknown	bulk	unknown	unknown	United States	2022-08-22	Undetermined	Multi-stage	Heart	Cardiovascular System
72819	72819	SRR23190058	SRX19140398	SRS16550346	SRP418629	PRJNA926357	Single cell transcriptional profiles of endothelial cells sorted from the hearts with ablation of Wnt/beta catenin signaling activating cardiomyocytes and without xxx [scRNA seq]	GSE223461	Transcriptome Analysis	To understand how Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs promote coronary vessel development we performed single cell RNA sequencing of endothelial cells ECs sorted from the hearts ablated ß cat ON CMs and those from control hearts respectively. Our analyses indicated that ß cat ON CMs regulates coronary vessel development by promoting arterialization a step in the transition of endocardial ECs to coronary ECs. Overall design: To induce nitroreductase metronidazole NTR MTZ dependent ablation of ß cat ON CMs we treated 5 mM MTZ or DMSO to Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish every other day for 4 weeks from 1 mpf. We isolated live GFP+ cells by FACS sorting from the fish treated MTZ or DMSO respectively. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.	parent bioproject:PRJNA926354	pubmed:39395410	EC MTZ scRNAseq	GSM6956592	source name:Heart\|tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:MTZ	EC MTZ scRNAseq	The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample	Heart	Fish were treated with DMSO or 5 mM MTZ dissolved in fish water for 12 h in the dark. post exposure to chemicals the water was changed to remove the chemicals and the fish were kept in the tank without xxx circulation. Chemicals were treated every other day.	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics 1000128 according to the manufacturer’s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.		tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:MTZ	GSM6956592	GSM6956592: EC MTZ scRNAseq; Danio rerio; RNA Seq	GSM6956592 r1	GSM6956592	1	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418629	loader:fastq load.py\|options: readTypes=BBTT read1PairFiles=M S1 L001 R1 001.fastq.gz read2PairFiles=M S1 L001 R2 001.fastq.gz read3PairFiles=M S1 L001 I1 001.fastq.gz read4PairFiles=M S1 L001 I2 001.fastq.gz	M_S1_L001_I1_001.fastq.gz M_S1_L001_I2_001.fastq.gz M_S1_L001_R1_001.fastq.gz M_S1_L001_R2_001.fastq.gz	fastq fastq fastq fastq	10297935498.0	74622721.0	GSM6956592 r1	0:28 1:90 2:10 3:10	A:2422395373;C:2014936837;G:2115011813;T:2251686635;N:1450420	28	90	10	10	2422395373	2014936837	2115011813	2251686635	1450420	SRX19140398	SRS16550346	SRA1578143	Department of Pharmacology, Yamagata University	Department of Pharmacology, Yamagata University	2	0.01687	0.92938	0.00583	0.17709	0.98549	0.82603	0.28254	0.55599	28	90	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Japan	2023-01-22	Multi-stage	Multi-stage	Heart	Cardiovascular System
72820	72820	SRR23190059	SRX19140398	SRS16550346	SRP418629	PRJNA926357	Single cell transcriptional profiles of endothelial cells sorted from the hearts with ablation of Wnt/beta catenin signaling activating cardiomyocytes and without xxx [scRNA seq]	GSE223461	Transcriptome Analysis	To understand how Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs promote coronary vessel development we performed single cell RNA sequencing of endothelial cells ECs sorted from the hearts ablated ß cat ON CMs and those from control hearts respectively. Our analyses indicated that ß cat ON CMs regulates coronary vessel development by promoting arterialization a step in the transition of endocardial ECs to coronary ECs. Overall design: To induce nitroreductase metronidazole NTR MTZ dependent ablation of ß cat ON CMs we treated 5 mM MTZ or DMSO to Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish every other day for 4 weeks from 1 mpf. We isolated live GFP+ cells by FACS sorting from the fish treated MTZ or DMSO respectively. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.	parent bioproject:PRJNA926354	pubmed:39395410	EC MTZ scRNAseq	GSM6956592	source name:Heart\|tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:MTZ	EC MTZ scRNAseq	The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample	Heart	Fish were treated with DMSO or 5 mM MTZ dissolved in fish water for 12 h in the dark. post exposure to chemicals the water was changed to remove the chemicals and the fish were kept in the tank without xxx circulation. Chemicals were treated every other day.	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics 1000128 according to the manufacturer’s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.		tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:MTZ	GSM6956592	GSM6956592: EC MTZ scRNAseq; Danio rerio; RNA Seq	GSM6956592 r1	GSM6956592	1	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418629	loader:fastq load.py\|options: readTypes=BBTT read1PairFiles=M S1 L002 R1 001.fastq.gz read2PairFiles=M S1 L002 R2 001.fastq.gz read3PairFiles=M S1 L002 I1 001.fastq.gz read4PairFiles=M S1 L002 I2 001.fastq.gz	M_S1_L002_I1_001.fastq.gz M_S1_L002_I2_001.fastq.gz M_S1_L002_R1_001.fastq.gz M_S1_L002_R2_001.fastq.gz	fastq fastq fastq fastq	10255307022.0	74313819.0	GSM6956592 r2	0:28 1:90 2:10 3:10	A:2413672015;C:2007739816;G:2105898639;T:2240007297;N:1712875	28	90	10	10	2413672015	2007739816	2105898639	2240007297	1712875	SRX19140398	SRS16550346	SRA1578143	Department of Pharmacology, Yamagata University	Department of Pharmacology, Yamagata University	2	0.01711	0.93111	0.00583	0.17637	0.98514	0.82639	0.27373	0.56532	28	90	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Japan	2023-01-22	Multi-stage	Multi-stage	Heart	Cardiovascular System
72821	72821	SRR23190060	SRX19140398	SRS16550346	SRP418629	PRJNA926357	Single cell transcriptional profiles of endothelial cells sorted from the hearts with ablation of Wnt/beta catenin signaling activating cardiomyocytes and without xxx [scRNA seq]	GSE223461	Transcriptome Analysis	To understand how Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs promote coronary vessel development we performed single cell RNA sequencing of endothelial cells ECs sorted from the hearts ablated ß cat ON CMs and those from control hearts respectively. Our analyses indicated that ß cat ON CMs regulates coronary vessel development by promoting arterialization a step in the transition of endocardial ECs to coronary ECs. Overall design: To induce nitroreductase metronidazole NTR MTZ dependent ablation of ß cat ON CMs we treated 5 mM MTZ or DMSO to Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish every other day for 4 weeks from 1 mpf. We isolated live GFP+ cells by FACS sorting from the fish treated MTZ or DMSO respectively. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.	parent bioproject:PRJNA926354	pubmed:39395410	EC MTZ scRNAseq	GSM6956592	source name:Heart\|tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:MTZ	EC MTZ scRNAseq	The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample	Heart	Fish were treated with DMSO or 5 mM MTZ dissolved in fish water for 12 h in the dark. post exposure to chemicals the water was changed to remove the chemicals and the fish were kept in the tank without xxx circulation. Chemicals were treated every other day.	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics 1000128 according to the manufacturer’s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.		tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:MTZ	GSM6956592	GSM6956592: EC MTZ scRNAseq; Danio rerio; RNA Seq	GSM6956592 r1	GSM6956592	1	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418629	loader:fastq load.py\|options: readTypes=BBTT read1PairFiles=M S1 L003 R1 001.fastq.gz read2PairFiles=M S1 L003 R2 001.fastq.gz read3PairFiles=M S1 L003 I1 001.fastq.gz read4PairFiles=M S1 L003 I2 001.fastq.gz	M_S1_L003_I1_001.fastq.gz M_S1_L003_I2_001.fastq.gz M_S1_L003_R1_001.fastq.gz M_S1_L003_R2_001.fastq.gz	fastq fastq fastq fastq	10416242898.0	75480021.0	GSM6956592 r3	0:28 1:90 2:10 3:10	A:2449287942;C:2038757909;G:2142133631;T:2275795705;N:667291	28	90	10	10	2449287942	2038757909	2142133631	2275795705	667291	SRX19140398	SRS16550346	SRA1578143	Department of Pharmacology, Yamagata University	Department of Pharmacology, Yamagata University	2	0.01658	0.92887	0.00568	0.17653	0.98593	0.82795	0.28335	0.55226	28	90	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Japan	2023-01-22	Multi-stage	Multi-stage	Heart	Cardiovascular System
72822	72822	SRR23190061	SRX19140398	SRS16550346	SRP418629	PRJNA926357	Single cell transcriptional profiles of endothelial cells sorted from the hearts with ablation of Wnt/beta catenin signaling activating cardiomyocytes and without xxx [scRNA seq]	GSE223461	Transcriptome Analysis	To understand how Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs promote coronary vessel development we performed single cell RNA sequencing of endothelial cells ECs sorted from the hearts ablated ß cat ON CMs and those from control hearts respectively. Our analyses indicated that ß cat ON CMs regulates coronary vessel development by promoting arterialization a step in the transition of endocardial ECs to coronary ECs. Overall design: To induce nitroreductase metronidazole NTR MTZ dependent ablation of ß cat ON CMs we treated 5 mM MTZ or DMSO to Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish every other day for 4 weeks from 1 mpf. We isolated live GFP+ cells by FACS sorting from the fish treated MTZ or DMSO respectively. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.	parent bioproject:PRJNA926354	pubmed:39395410	EC MTZ scRNAseq	GSM6956592	source name:Heart\|tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:MTZ	EC MTZ scRNAseq	The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample	Heart	Fish were treated with DMSO or 5 mM MTZ dissolved in fish water for 12 h in the dark. post exposure to chemicals the water was changed to remove the chemicals and the fish were kept in the tank without xxx circulation. Chemicals were treated every other day.	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics 1000128 according to the manufacturer’s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.		tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:MTZ	GSM6956592	GSM6956592: EC MTZ scRNAseq; Danio rerio; RNA Seq	GSM6956592 r1	GSM6956592	1	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418629	loader:fastq load.py\|options: readTypes=BBTT read1PairFiles=M S1 L004 R1 001.fastq.gz read2PairFiles=M S1 L004 R2 001.fastq.gz read3PairFiles=M S1 L004 I1 001.fastq.gz read4PairFiles=M S1 L004 I2 001.fastq.gz	M_S1_L004_I1_001.fastq.gz M_S1_L004_I2_001.fastq.gz M_S1_L004_R1_001.fastq.gz M_S1_L004_R2_001.fastq.gz	fastq fastq fastq fastq	10441110360.0	75660220.0	GSM6956592 r4	0:28 1:90 2:10 3:10	A:2455796397;C:2044932269;G:2145932306;T:2280585820;N:659168	28	90	10	10	2455796397	2044932269	2145932306	2280585820	659168	SRX19140398	SRS16550346	SRA1578143	Department of Pharmacology, Yamagata University	Department of Pharmacology, Yamagata University	2	0.01734	0.92942	0.00594	0.17578	0.98502	0.82605	0.27199	0.55089	28	90	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Japan	2023-01-22	Multi-stage	Multi-stage	Heart	Cardiovascular System
72823	72823	SRR23190062	SRX19140397	SRS16550345	SRP418629	PRJNA926357	Single cell transcriptional profiles of endothelial cells sorted from the hearts with ablation of Wnt/beta catenin signaling activating cardiomyocytes and without xxx [scRNA seq]	GSE223461	Transcriptome Analysis	To understand how Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs promote coronary vessel development we performed single cell RNA sequencing of endothelial cells ECs sorted from the hearts ablated ß cat ON CMs and those from control hearts respectively. Our analyses indicated that ß cat ON CMs regulates coronary vessel development by promoting arterialization a step in the transition of endocardial ECs to coronary ECs. Overall design: To induce nitroreductase metronidazole NTR MTZ dependent ablation of ß cat ON CMs we treated 5 mM MTZ or DMSO to Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish every other day for 4 weeks from 1 mpf. We isolated live GFP+ cells by FACS sorting from the fish treated MTZ or DMSO respectively. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.	parent bioproject:PRJNA926354	pubmed:39395410	EC DMSO scRNAseq	GSM6956591	source name:Heart\|tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:DMSO	EC DMSO scRNAseq	The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample	Heart	Fish were treated with DMSO or 5 mM MTZ dissolved in fish water for 12 h in the dark. post exposure to chemicals the water was changed to remove the chemicals and the fish were kept in the tank without xxx circulation. Chemicals were treated every other day.	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics 1000128 according to the manufacturer’s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.		tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:DMSO	GSM6956591	GSM6956591: EC DMSO scRNAseq; Danio rerio; RNA Seq	GSM6956591 r1	GSM6956591	1	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418629	loader:fastq load.py\|options: readTypes=BBTT read1PairFiles=D S1 L001 R1 001.fastq.gz read2PairFiles=D S1 L001 R2 001.fastq.gz read3PairFiles=D S1 L001 I1 001.fastq.gz read4PairFiles=D S1 L001 I2 001.fastq.gz	D_S1_L001_I1_001.fastq.gz D_S1_L001_I2_001.fastq.gz D_S1_L001_R1_001.fastq.gz D_S1_L001_R2_001.fastq.gz	fastq fastq fastq fastq	10595595012.0	76779674.0	GSM6956591 r1	0:28 1:90 2:10 3:10	A:2544857509;C:2041473878;G:2166945643;T:2305102603;N:1621899	28	90	10	10	2544857509	2041473878	2166945643	2305102603	1621899	SRX19140397	SRS16550345	SRA1578143	Department of Pharmacology, Yamagata University	Department of Pharmacology, Yamagata University	2	0.01657	0.92608	0.00601	0.18008	0.98602	0.82844	0.27705	0.55772	28	90	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Japan	2023-01-22	Multi-stage	Multi-stage	Heart	Cardiovascular System
72824	72824	SRR23190063	SRX19140397	SRS16550345	SRP418629	PRJNA926357	Single cell transcriptional profiles of endothelial cells sorted from the hearts with ablation of Wnt/beta catenin signaling activating cardiomyocytes and without xxx [scRNA seq]	GSE223461	Transcriptome Analysis	To understand how Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs promote coronary vessel development we performed single cell RNA sequencing of endothelial cells ECs sorted from the hearts ablated ß cat ON CMs and those from control hearts respectively. Our analyses indicated that ß cat ON CMs regulates coronary vessel development by promoting arterialization a step in the transition of endocardial ECs to coronary ECs. Overall design: To induce nitroreductase metronidazole NTR MTZ dependent ablation of ß cat ON CMs we treated 5 mM MTZ or DMSO to Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish every other day for 4 weeks from 1 mpf. We isolated live GFP+ cells by FACS sorting from the fish treated MTZ or DMSO respectively. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.	parent bioproject:PRJNA926354	pubmed:39395410	EC DMSO scRNAseq	GSM6956591	source name:Heart\|tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:DMSO	EC DMSO scRNAseq	The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample	Heart	Fish were treated with DMSO or 5 mM MTZ dissolved in fish water for 12 h in the dark. post exposure to chemicals the water was changed to remove the chemicals and the fish were kept in the tank without xxx circulation. Chemicals were treated every other day.	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics 1000128 according to the manufacturer’s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.		tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:DMSO	GSM6956591	GSM6956591: EC DMSO scRNAseq; Danio rerio; RNA Seq	GSM6956591 r1	GSM6956591	1	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418629	loader:fastq load.py\|options: readTypes=BBTT read1PairFiles=D S1 L002 R1 001.fastq.gz read2PairFiles=D S1 L002 R2 001.fastq.gz read3PairFiles=D S1 L002 I1 001.fastq.gz read4PairFiles=D S1 L002 I2 001.fastq.gz	D_S1_L002_I1_001.fastq.gz D_S1_L002_I2_001.fastq.gz D_S1_L002_R1_001.fastq.gz D_S1_L002_R2_001.fastq.gz	fastq fastq fastq fastq	10505133804.0	76124158.0	GSM6956591 r2	0:28 1:90 2:10 3:10	A:2524419025;C:2024371965;G:2148601948;T:2283479741;N:1777965	28	90	10	10	2524419025	2024371965	2148601948	2283479741	1777965	SRX19140397	SRS16550345	SRA1578143	Department of Pharmacology, Yamagata University	Department of Pharmacology, Yamagata University	2	0.01639	0.92559	0.00547	0.17815	0.98524	0.83004	0.2875	0.56427	28	90	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Japan	2023-01-22	Multi-stage	Multi-stage	Heart	Cardiovascular System
72825	72825	SRR23190064	SRX19140397	SRS16550345	SRP418629	PRJNA926357	Single cell transcriptional profiles of endothelial cells sorted from the hearts with ablation of Wnt/beta catenin signaling activating cardiomyocytes and without xxx [scRNA seq]	GSE223461	Transcriptome Analysis	To understand how Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs promote coronary vessel development we performed single cell RNA sequencing of endothelial cells ECs sorted from the hearts ablated ß cat ON CMs and those from control hearts respectively. Our analyses indicated that ß cat ON CMs regulates coronary vessel development by promoting arterialization a step in the transition of endocardial ECs to coronary ECs. Overall design: To induce nitroreductase metronidazole NTR MTZ dependent ablation of ß cat ON CMs we treated 5 mM MTZ or DMSO to Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish every other day for 4 weeks from 1 mpf. We isolated live GFP+ cells by FACS sorting from the fish treated MTZ or DMSO respectively. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.	parent bioproject:PRJNA926354	pubmed:39395410	EC DMSO scRNAseq	GSM6956591	source name:Heart\|tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:DMSO	EC DMSO scRNAseq	The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample	Heart	Fish were treated with DMSO or 5 mM MTZ dissolved in fish water for 12 h in the dark. post exposure to chemicals the water was changed to remove the chemicals and the fish were kept in the tank without xxx circulation. Chemicals were treated every other day.	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics 1000128 according to the manufacturer’s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.		tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:DMSO	GSM6956591	GSM6956591: EC DMSO scRNAseq; Danio rerio; RNA Seq	GSM6956591 r1	GSM6956591	1	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418629	loader:fastq load.py\|options: readTypes=BBTT read1PairFiles=D S1 L003 R1 001.fastq.gz read2PairFiles=D S1 L003 R2 001.fastq.gz read3PairFiles=D S1 L003 I1 001.fastq.gz read4PairFiles=D S1 L003 I2 001.fastq.gz	D_S1_L003_I1_001.fastq.gz D_S1_L003_I2_001.fastq.gz D_S1_L003_R1_001.fastq.gz D_S1_L003_R2_001.fastq.gz	fastq fastq fastq fastq	10715702622.0	77650019.0	GSM6956591 r3	0:28 1:90 2:10 3:10	A:2573807593;C:2065042721;G:2193827962;T:2329228642;N:795324	28	90	10	10	2573807593	2065042721	2193827962	2329228642	795324	SRX19140397	SRS16550345	SRA1578143	Department of Pharmacology, Yamagata University	Department of Pharmacology, Yamagata University	2	0.0164	0.92651	0.00558	0.17924	0.98559	0.82816	0.27685	0.56637	28	90	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Japan	2023-01-22	Multi-stage	Multi-stage	Heart	Cardiovascular System
72826	72826	SRR23190065	SRX19140397	SRS16550345	SRP418629	PRJNA926357	Single cell transcriptional profiles of endothelial cells sorted from the hearts with ablation of Wnt/beta catenin signaling activating cardiomyocytes and without xxx [scRNA seq]	GSE223461	Transcriptome Analysis	To understand how Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs promote coronary vessel development we performed single cell RNA sequencing of endothelial cells ECs sorted from the hearts ablated ß cat ON CMs and those from control hearts respectively. Our analyses indicated that ß cat ON CMs regulates coronary vessel development by promoting arterialization a step in the transition of endocardial ECs to coronary ECs. Overall design: To induce nitroreductase metronidazole NTR MTZ dependent ablation of ß cat ON CMs we treated 5 mM MTZ or DMSO to Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish every other day for 4 weeks from 1 mpf. We isolated live GFP+ cells by FACS sorting from the fish treated MTZ or DMSO respectively. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.	parent bioproject:PRJNA926354	pubmed:39395410	EC DMSO scRNAseq	GSM6956591	source name:Heart\|tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:DMSO	EC DMSO scRNAseq	The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample	Heart	Fish were treated with DMSO or 5 mM MTZ dissolved in fish water for 12 h in the dark. post exposure to chemicals the water was changed to remove the chemicals and the fish were kept in the tank without xxx circulation. Chemicals were treated every other day.	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics 1000128 according to the manufacturer’s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.		tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:DMSO	GSM6956591	GSM6956591: EC DMSO scRNAseq; Danio rerio; RNA Seq	GSM6956591 r1	GSM6956591	1	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418629	loader:fastq load.py\|options: readTypes=BBTT read1PairFiles=D S1 L004 R1 001.fastq.gz read2PairFiles=D S1 L004 R2 001.fastq.gz read3PairFiles=D S1 L004 I1 001.fastq.gz read4PairFiles=D S1 L004 I2 001.fastq.gz	D_S1_L004_I1_001.fastq.gz D_S1_L004_I2_001.fastq.gz D_S1_L004_R1_001.fastq.gz D_S1_L004_R2_001.fastq.gz	fastq fastq fastq fastq	10731126882.0	77761789.0	GSM6956591 r4	0:28 1:90 2:10 3:10	A:2577638514;C:2068754148;G:2196571470;T:2332228096;N:698874	28	90	10	10	2577638514	2068754148	2196571470	2332228096	698874	SRX19140397	SRS16550345	SRA1578143	Department of Pharmacology, Yamagata University	Department of Pharmacology, Yamagata University	2	0.01687	0.9273	0.00577	0.18031	0.98476	0.82954	0.28103	0.55337	28	90	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Japan	2023-01-22	Multi-stage	Multi-stage	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");;