metadata: run_metadata: 66 rows where experiment.platform = "ILLUMINA", technology = "generic-scrnaseq-only" and tissue_curation

66 rows where experiment.platform = "ILLUMINA", technology = "generic-scrnaseq-only" and tissue_curation_coarse = "Cardiovascular System"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.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.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
41355	41355	SRR4342171	SRX2209226	SRS1726586	SRP090801	PRJNA345325	Comparison of tbx5 positive ventricular cardiomyoctes with the rest of ventricular cardiomyocytes from adult zebrafish hearts	GSE87596	Transcriptome Analysis	In vertebrates the heart has two main layers of cardiac muscle a peripheral compact layer and an internal trabecular layer. Little is known on the differerences in gene expression between both layers. In zebrafish the outer layer is named cortical layer and the internal also trabecular layer. Here we used a double transgenic line labelling with GFP tbx5 positive cells and cardiomyoctes with nuclear DsRed nucDsRed to distinguish cortical from trabecular myocardium. Then we compared the transcriptome of trabecular and cortical myocardium in the adult zebrafish. We describe that Tbx5a is a good marker of trabecular myocardium. Overall design: Four paired biological replicates consisting on Tbx5 positive and Tbx5 negative adult zebrafish ventricular cardiomyocytes were analysed by RNA seq to compare their transcriptomic profiles.		pubmed:29382818	tbx5 9pos	GSM2334964	source name:Heart\|age:Adult\|tissue:Heart\|cell type:Tbx5 positive ventricular cardiomyocytes\|pair:9	tbx5 9pos	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	GFP/nucDsRed and nucDsRed cells were isolated using FAC sorting from Tgtbx5:GFP/myl7:nucDsRed double transgenic adult zebrafish cardiac ventricles. Cells were sorted using SONY Synergy sy3200.	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	age:Adult\|tissue:Heart\|cell type:Tbx5 positive ventricular cardiomyocytes\|pair:9	GSM2334964	GSM2334964: tbx5 9pos; Danio rerio; RNA Seq	GSM2334964		1	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	GEO Accession:GSM2334964	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP090801	tbx5_9pos__HectorSanchez_RNA_Seq_OvationSC_ACCTCA_L002_R1_001.fastq.gz	fastq	783131298.0	12838218.0	GSM2334964 r1	0:61	A:231794213;C:152686156;G:196289761;T:202337851;N:23317	61		231794213	152686156	196289761	202337851	23317	SRX2209226	SRS1726586	SRA481772	GEO	Bioinformatics Unit, CNIC	1	0.91274		0.14772		0.85084		0.58033		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2016-10-04	Adult	Adult	Heart	Cardiovascular System
41356	41356	SRR4342170	SRX2209225	SRS1726587	SRP090801	PRJNA345325	Comparison of tbx5 positive ventricular cardiomyoctes with the rest of ventricular cardiomyocytes from adult zebrafish hearts	GSE87596	Transcriptome Analysis	In vertebrates the heart has two main layers of cardiac muscle a peripheral compact layer and an internal trabecular layer. Little is known on the differerences in gene expression between both layers. In zebrafish the outer layer is named cortical layer and the internal also trabecular layer. Here we used a double transgenic line labelling with GFP tbx5 positive cells and cardiomyoctes with nuclear DsRed nucDsRed to distinguish cortical from trabecular myocardium. Then we compared the transcriptome of trabecular and cortical myocardium in the adult zebrafish. We describe that Tbx5a is a good marker of trabecular myocardium. Overall design: Four paired biological replicates consisting on Tbx5 positive and Tbx5 negative adult zebrafish ventricular cardiomyocytes were analysed by RNA seq to compare their transcriptomic profiles.		pubmed:29382818	tbx5 9neg	GSM2334963	source name:Heart\|age:Adult\|tissue:Heart\|cell type:Tbx5 negative ventricular cardiomyocytes\|pair:9	tbx5 9neg	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	GFP/nucDsRed and nucDsRed cells were isolated using FAC sorting from Tgtbx5:GFP/myl7:nucDsRed double transgenic adult zebrafish cardiac ventricles. Cells were sorted using SONY Synergy sy3200.	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	age:Adult\|tissue:Heart\|cell type:Tbx5 negative ventricular cardiomyocytes\|pair:9	GSM2334963	GSM2334963: tbx5 9neg; Danio rerio; RNA Seq	GSM2334963		1	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	GEO Accession:GSM2334963	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP090801	tbx5_9neg__HectorSanchez_RNA_Seq_OvationSC_GTGCTT_L002_R1_001.fastq.gz	fastq	597229833.0	9790653.0	GSM2334963 r1	0:61	A:182072130;C:116058906;G:143260521;T:155820528;N:17748	61		182072130	116058906	143260521	155820528	17748	SRX2209225	SRS1726587	SRA481772	GEO	Bioinformatics Unit, CNIC	1	0.8964		0.14551		0.85612		0.54858		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2016-10-04	Adult	Adult	Heart	Cardiovascular System
41357	41357	SRR4342169	SRX2209224	SRS1726585	SRP090801	PRJNA345325	Comparison of tbx5 positive ventricular cardiomyoctes with the rest of ventricular cardiomyocytes from adult zebrafish hearts	GSE87596	Transcriptome Analysis	In vertebrates the heart has two main layers of cardiac muscle a peripheral compact layer and an internal trabecular layer. Little is known on the differerences in gene expression between both layers. In zebrafish the outer layer is named cortical layer and the internal also trabecular layer. Here we used a double transgenic line labelling with GFP tbx5 positive cells and cardiomyoctes with nuclear DsRed nucDsRed to distinguish cortical from trabecular myocardium. Then we compared the transcriptome of trabecular and cortical myocardium in the adult zebrafish. We describe that Tbx5a is a good marker of trabecular myocardium. Overall design: Four paired biological replicates consisting on Tbx5 positive and Tbx5 negative adult zebrafish ventricular cardiomyocytes were analysed by RNA seq to compare their transcriptomic profiles.		pubmed:29382818	tbx5 8pos	GSM2334962	source name:Heart\|age:Adult\|tissue:Heart\|cell type:Tbx5 positive ventricular cardiomyocytes\|pair:8	tbx5 8pos	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	GFP/nucDsRed and nucDsRed cells were isolated using FAC sorting from Tgtbx5:GFP/myl7:nucDsRed double transgenic adult zebrafish cardiac ventricles. Cells were sorted using SONY Synergy sy3200.	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	age:Adult\|tissue:Heart\|cell type:Tbx5 positive ventricular cardiomyocytes\|pair:8	GSM2334962	GSM2334962: tbx5 8pos; Danio rerio; RNA Seq	GSM2334962		1	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	GEO Accession:GSM2334962	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP090801	tbx5_8pos__HectorSanchez_RNA_Seq_OvationSC_AGTGAG_L001_R1_001.fastq.gz	fastq	749298746.0	12283586.0	GSM2334962 r1	0:61	A:223933431;C:143222641;G:189173448;T:192959794;N:9432	61		223933431	143222641	189173448	192959794	9432	SRX2209224	SRS1726585	SRA481772	GEO	Bioinformatics Unit, CNIC	1	0.91034		0.13718		0.85192		0.56656		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2016-10-04	Adult	Adult	Heart	Cardiovascular System
41358	41358	SRR4342168	SRX2209223	SRS1726584	SRP090801	PRJNA345325	Comparison of tbx5 positive ventricular cardiomyoctes with the rest of ventricular cardiomyocytes from adult zebrafish hearts	GSE87596	Transcriptome Analysis	In vertebrates the heart has two main layers of cardiac muscle a peripheral compact layer and an internal trabecular layer. Little is known on the differerences in gene expression between both layers. In zebrafish the outer layer is named cortical layer and the internal also trabecular layer. Here we used a double transgenic line labelling with GFP tbx5 positive cells and cardiomyoctes with nuclear DsRed nucDsRed to distinguish cortical from trabecular myocardium. Then we compared the transcriptome of trabecular and cortical myocardium in the adult zebrafish. We describe that Tbx5a is a good marker of trabecular myocardium. Overall design: Four paired biological replicates consisting on Tbx5 positive and Tbx5 negative adult zebrafish ventricular cardiomyocytes were analysed by RNA seq to compare their transcriptomic profiles.		pubmed:29382818	tbx5 8neg	GSM2334961	source name:Heart\|age:Adult\|tissue:Heart\|cell type:Tbx5 negative ventricular cardiomyocytes\|pair:8	tbx5 8neg	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	GFP/nucDsRed and nucDsRed cells were isolated using FAC sorting from Tgtbx5:GFP/myl7:nucDsRed double transgenic adult zebrafish cardiac ventricles. Cells were sorted using SONY Synergy sy3200.	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	age:Adult\|tissue:Heart\|cell type:Tbx5 negative ventricular cardiomyocytes\|pair:8	GSM2334961	GSM2334961: tbx5 8neg; Danio rerio; RNA Seq	GSM2334961		1	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	GEO Accession:GSM2334961	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP090801	tbx5_8neg__HectorSanchez_RNA_Seq_OvationSC_GCACTA_L001_R1_001.fastq.gz	fastq	671219417.0	11003597.0	GSM2334961 r1	0:61	A:200873049;C:127618001;G:167285388;T:175434453;N:8526	61		200873049	127618001	167285388	175434453	8526	SRX2209223	SRS1726584	SRA481772	GEO	Bioinformatics Unit, CNIC	1	0.89809		0.15716		0.84634		0.55363		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2016-10-04	Adult	Adult	Heart	Cardiovascular System
41359	41359	SRR4342167	SRX2209222	SRS1726583	SRP090801	PRJNA345325	Comparison of tbx5 positive ventricular cardiomyoctes with the rest of ventricular cardiomyocytes from adult zebrafish hearts	GSE87596	Transcriptome Analysis	In vertebrates the heart has two main layers of cardiac muscle a peripheral compact layer and an internal trabecular layer. Little is known on the differerences in gene expression between both layers. In zebrafish the outer layer is named cortical layer and the internal also trabecular layer. Here we used a double transgenic line labelling with GFP tbx5 positive cells and cardiomyoctes with nuclear DsRed nucDsRed to distinguish cortical from trabecular myocardium. Then we compared the transcriptome of trabecular and cortical myocardium in the adult zebrafish. We describe that Tbx5a is a good marker of trabecular myocardium. Overall design: Four paired biological replicates consisting on Tbx5 positive and Tbx5 negative adult zebrafish ventricular cardiomyocytes were analysed by RNA seq to compare their transcriptomic profiles.		pubmed:29382818	tbx5 2pos	GSM2334960	source name:Heart\|age:Adult\|tissue:Heart\|cell type:Tbx5 positive ventricular cardiomyocytes\|pair:2	tbx5 2pos	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	GFP/nucDsRed and nucDsRed cells were isolated using FAC sorting from Tgtbx5:GFP/myl7:nucDsRed double transgenic adult zebrafish cardiac ventricles. Cells were sorted using SONY Synergy sy3200.	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	age:Adult\|tissue:Heart\|cell type:Tbx5 positive ventricular cardiomyocytes\|pair:2	GSM2334960	GSM2334960: tbx5 2pos; Danio rerio; RNA Seq	GSM2334960		1	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	GEO Accession:GSM2334960	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP090801	tbx5_2pos__HectorSanchez_RNA_Seq_OvationSC_AACCAG_L001_R1_001.fastq.gz	fastq	721753525.0	11832025.0	GSM2334960 r1	0:61	A:210172867;C:139636671;G:184046654;T:187888215;N:9118	61		210172867	139636671	184046654	187888215	9118	SRX2209222	SRS1726583	SRA481772	GEO	Bioinformatics Unit, CNIC	1	0.88264		0.17411		0.85027		0.50468		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2016-10-04	Adult	Adult	Heart	Cardiovascular System
41360	41360	SRR4342166	SRX2209221	SRS1726581	SRP090801	PRJNA345325	Comparison of tbx5 positive ventricular cardiomyoctes with the rest of ventricular cardiomyocytes from adult zebrafish hearts	GSE87596	Transcriptome Analysis	In vertebrates the heart has two main layers of cardiac muscle a peripheral compact layer and an internal trabecular layer. Little is known on the differerences in gene expression between both layers. In zebrafish the outer layer is named cortical layer and the internal also trabecular layer. Here we used a double transgenic line labelling with GFP tbx5 positive cells and cardiomyoctes with nuclear DsRed nucDsRed to distinguish cortical from trabecular myocardium. Then we compared the transcriptome of trabecular and cortical myocardium in the adult zebrafish. We describe that Tbx5a is a good marker of trabecular myocardium. Overall design: Four paired biological replicates consisting on Tbx5 positive and Tbx5 negative adult zebrafish ventricular cardiomyocytes were analysed by RNA seq to compare their transcriptomic profiles.		pubmed:29382818	tbx5 2neg	GSM2334959	source name:Heart\|age:Adult\|tissue:Heart\|cell type:Tbx5 negative ventricular cardiomyocytes\|pair:2	tbx5 2neg	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	GFP/nucDsRed and nucDsRed cells were isolated using FAC sorting from Tgtbx5:GFP/myl7:nucDsRed double transgenic adult zebrafish cardiac ventricles. Cells were sorted using SONY Synergy sy3200.	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	age:Adult\|tissue:Heart\|cell type:Tbx5 negative ventricular cardiomyocytes\|pair:2	GSM2334959	GSM2334959: tbx5 2neg; Danio rerio; RNA Seq	GSM2334959		1	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	GEO Accession:GSM2334959	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP090801	tbx5_2neg__HectorSanchez_RNA_Seq_OvationSC_TGGTGA_L001_R1_001.fastq.gz	fastq	719361654.0	11792814.0	GSM2334959 r1	0:61	A:210895656;C:137890002;G:180431743;T:190135096;N:9157	61		210895656	137890002	180431743	190135096	9157	SRX2209221	SRS1726581	SRA481772	GEO	Bioinformatics Unit, CNIC	1	0.76636		0.15624		0.8547		0.52604		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2016-10-04	Adult	Adult	Heart	Cardiovascular System
41361	41361	SRR4342165	SRX2209220	SRS1726582	SRP090801	PRJNA345325	Comparison of tbx5 positive ventricular cardiomyoctes with the rest of ventricular cardiomyocytes from adult zebrafish hearts	GSE87596	Transcriptome Analysis	In vertebrates the heart has two main layers of cardiac muscle a peripheral compact layer and an internal trabecular layer. Little is known on the differerences in gene expression between both layers. In zebrafish the outer layer is named cortical layer and the internal also trabecular layer. Here we used a double transgenic line labelling with GFP tbx5 positive cells and cardiomyoctes with nuclear DsRed nucDsRed to distinguish cortical from trabecular myocardium. Then we compared the transcriptome of trabecular and cortical myocardium in the adult zebrafish. We describe that Tbx5a is a good marker of trabecular myocardium. Overall design: Four paired biological replicates consisting on Tbx5 positive and Tbx5 negative adult zebrafish ventricular cardiomyocytes were analysed by RNA seq to compare their transcriptomic profiles.		pubmed:29382818	tbx5 10pos	GSM2334958	source name:Heart\|age:Adult\|tissue:Heart\|cell type:Tbx5 positive ventricular cardiomyocytes\|pair:10	tbx5 10pos	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	GFP/nucDsRed and nucDsRed cells were isolated using FAC sorting from Tgtbx5:GFP/myl7:nucDsRed double transgenic adult zebrafish cardiac ventricles. Cells were sorted using SONY Synergy sy3200.	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	age:Adult\|tissue:Heart\|cell type:Tbx5 positive ventricular cardiomyocytes\|pair:10	GSM2334958	GSM2334958: tbx5 10pos; Danio rerio; RNA Seq	GSM2334958		1	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	GEO Accession:GSM2334958	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP090801	tbx5_10pos__HectorSanchez_RNA_Seq_OvationSC_AAGCCT_L002_R1_001.fastq.gz	fastq	754707555.0	12372255.0	GSM2334958 r1	0:61	A:221942809;C:151029762;G:190399372;T:191312963;N:22649	61		221942809	151029762	190399372	191312963	22649	SRX2209220	SRS1726582	SRA481772	GEO	Bioinformatics Unit, CNIC	1	0.92066		0.11265		0.85121		0.57097		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2016-10-04	Adult	Adult	Heart	Cardiovascular System
41362	41362	SRR4342164	SRX2209219	SRS1726580	SRP090801	PRJNA345325	Comparison of tbx5 positive ventricular cardiomyoctes with the rest of ventricular cardiomyocytes from adult zebrafish hearts	GSE87596	Transcriptome Analysis	In vertebrates the heart has two main layers of cardiac muscle a peripheral compact layer and an internal trabecular layer. Little is known on the differerences in gene expression between both layers. In zebrafish the outer layer is named cortical layer and the internal also trabecular layer. Here we used a double transgenic line labelling with GFP tbx5 positive cells and cardiomyoctes with nuclear DsRed nucDsRed to distinguish cortical from trabecular myocardium. Then we compared the transcriptome of trabecular and cortical myocardium in the adult zebrafish. We describe that Tbx5a is a good marker of trabecular myocardium. Overall design: Four paired biological replicates consisting on Tbx5 positive and Tbx5 negative adult zebrafish ventricular cardiomyocytes were analysed by RNA seq to compare their transcriptomic profiles.		pubmed:29382818	tbx5 10neg	GSM2334957	source name:Heart\|age:Adult\|tissue:Heart\|cell type:Tbx5 negative ventricular cardiomyocytes\|pair:10	tbx5 10neg	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	GFP/nucDsRed and nucDsRed cells were isolated using FAC sorting from Tgtbx5:GFP/myl7:nucDsRed double transgenic adult zebrafish cardiac ventricles. Cells were sorted using SONY Synergy sy3200.	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	age:Adult\|tissue:Heart\|cell type:Tbx5 negative ventricular cardiomyocytes\|pair:10	GSM2334957	GSM2334957: tbx5 10neg; Danio rerio; RNA Seq	GSM2334957		1	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	GEO Accession:GSM2334957	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP090801	tbx5_10neg__HectorSanchez_RNA_Seq_OvationSC_GTCGTA_L002_R1_001.fastq.gz	fastq	792684264.0	12994824.0	GSM2334957 r1	0:61	A:231862367;C:153096010;G:201328453;T:206373690;N:23744	61		231862367	153096010	201328453	206373690	23744	SRX2209219	SRS1726580	SRA481772	GEO	Bioinformatics Unit, CNIC	1	0.89586		0.16316		0.84435		0.53348		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2016-10-04	Adult	Adult	Heart	Cardiovascular System
42873	42873	SRR5817929	SRX2996183	SRS2347418	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343	neg 7dpi 10	GSM2700316	tissue:Heart\|cell type:kdrl:mCherry /postn:citrine \|treatment:7 xxx post injury\|pool:10	neg 7dpi 10	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:kdrl:mCherry /postn:citrine \|treatment:7 xxx post injury\|pool:10	GSM2700316	GSM2700316: neg 7dpi 10; Danio rerio; RNA Seq	GSM2700316		1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700316	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552	Neg_7dpi_10__HS_OvationSC_ACCTCA_L001_R1_001.fastq.gz	fastq	2259317756.0	37037996.0	GSM2700316 r1	0:61	A:593901686;C:479409193;G:663867943;T:522077484;N:61450	61		593901686	479409193	663867943	522077484	61450	SRX2996183	SRS2347418	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.78451		0.21243		0.79275		0.70146		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42874	42874	SRR5817928	SRX2996182	SRS2347417	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343	neg 7dpi 09	GSM2700315	tissue:Heart\|cell type:kdrl:mCherry /postn:citrine \|treatment:7 xxx post injury\|pool:9	neg 7dpi 09	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:kdrl:mCherry /postn:citrine \|treatment:7 xxx post injury\|pool:9	GSM2700315	GSM2700315: neg 7dpi 09; Danio rerio; RNA Seq	GSM2700315		1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700315	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552	Neg_7dpi_09__HS_OvationSC_AGTGAG_L001_R1_001.fastq.gz	fastq	1969074205.0	32279905.0	GSM2700315 r1	0:61	A:506203021;C:400192379;G:588278464;T:474347230;N:53111	61		506203021	400192379	588278464	474347230	53111	SRX2996182	SRS2347417	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.83786		0.24573		0.78979		0.69734		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42875	42875	SRR5817927	SRX2996181	SRS2347416	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343	neg 7dpi 08	GSM2700314	tissue:Heart\|cell type:kdrl:mCherry /postn:citrine \|treatment:7 xxx post injury\|pool:8	neg 7dpi 08	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:kdrl:mCherry /postn:citrine \|treatment:7 xxx post injury\|pool:8	GSM2700314	GSM2700314: neg 7dpi 08; Danio rerio; RNA Seq	GSM2700314		1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700314	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552	Neg_7dpi_08__HS_OvationSC_TCAGAG_L008_R1_001.fastq.gz	fastq	775093328.0	12706448.0	GSM2700314 r1	0:61	A:207451085;C:158380757;G:223015883;T:186233015;N:12588	61		207451085	158380757	223015883	186233015	12588	SRX2996181	SRS2347416	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.77247		0.24093		0.81142		0.61394		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42876	42876	SRR5817926	SRX2996180	SRS2347415	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343	neg 7dpi 07	GSM2700313	tissue:Heart\|cell type:kdrl:mCherry /postn:citrine \|treatment:7 xxx post injury\|pool:7	neg 7dpi 07	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:kdrl:mCherry /postn:citrine \|treatment:7 xxx post injury\|pool:7	GSM2700313	GSM2700313: neg 7dpi 07; Danio rerio; RNA Seq	GSM2700313		1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700313	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552	Neg_7dpi_07__HS_OvationSC_AGCATG_L008_R1_001.fastq.gz	fastq	667662873.0	10945293.0	GSM2700313 r1	0:61	A:184011441;C:129142619;G:186565080;T:167933144;N:10589	61		184011441	129142619	186565080	167933144	10589	SRX2996180	SRS2347415	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.78352		0.24932		0.79322		0.5843		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42877	42877	SRR5817925	SRX2996179	SRS2347414	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343	neg 7dpi 06	GSM2700312	tissue:Heart\|cell type:kdrl:mCherry /postn:citrine \|treatment:7 xxx post injury\|pool:6	neg 7dpi 06	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:kdrl:mCherry /postn:citrine \|treatment:7 xxx post injury\|pool:6	GSM2700312	GSM2700312: neg 7dpi 06; Danio rerio; RNA Seq	GSM2700312		1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700312	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552	Neg_7dpi_06__HS_OvationSC_GTCGTA_L007_R1_001.fastq.gz	fastq	1506843472.0	24702352.0	GSM2700312 r1	0:61	A:415665970;C:284643457;G:414417308;T:391840093;N:276644	61		415665970	284643457	414417308	391840093	276644	SRX2996179	SRS2347414	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.67862		0.21798		0.79419		0.56611		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42878	42878	SRR5817924	SRX2996178	SRS2347412	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343	neg 7dpi 05	GSM2700311	tissue:Heart\|cell type:kdrl:mCherry /postn:citrine \|treatment:7 xxx post injury\|pool:5	neg 7dpi 05	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:kdrl:mCherry /postn:citrine \|treatment:7 xxx post injury\|pool:5	GSM2700311	GSM2700311: neg 7dpi 05; Danio rerio; RNA Seq	GSM2700311		1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700311	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552	Neg_7dpi_05__HS_OvationSC_ACCTCA_L007_R1_001.fastq.gz	fastq	1170594758.0	19190078.0	GSM2700311 r1	0:61	A:304620201;C:245838062;G:349652017;T:270272581;N:211897	61		304620201	245838062	349652017	270272581	211897	SRX2996178	SRS2347412	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.81997		0.21036		0.81962		0.66201		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42879	42879	SRR5817923	SRX2996177	SRS2347413	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343	postnb citrine 7dpi 10	GSM2700310	tissue:Heart\|cell type:postnb:citrine+\|treatment:7 xxx post injury\|pool:10	postnb citrine 7dpi 10	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:postnb:citrine+\|treatment:7 xxx post injury\|pool:10	GSM2700310	GSM2700310: postnb citrine 7dpi 10; Danio rerio; RNA Seq	GSM2700310		1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700310	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552	postnb_7dpi_10__HS_OvationSC_GCACTA_L001_R1_001.fastq.gz	fastq	2252204790.0	36921390.0	GSM2700310 r1	0:61	A:619277021;C:502942463;G:646027370;T:483900520;N:57416	61		619277021	502942463	646027370	483900520	57416	SRX2996177	SRS2347413	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.57676		0.1734		0.83984		0.65906		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42880	42880	SRR5817922	SRX2996176	SRS2347410	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343	postnb citrine 7dpi 09	GSM2700309	tissue:Heart\|cell type:postnb:citrine+\|treatment:7 xxx post injury\|pool:9	postnb citrine 7dpi 09	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:postnb:citrine+\|treatment:7 xxx post injury\|pool:9	GSM2700309	GSM2700309: postnb citrine 7dpi 09; Danio rerio; RNA Seq	GSM2700309		1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700309	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552	postnb_7dpi_09__HS_OvationSC_AACCAG_L001_R1_001.fastq.gz	fastq	2283341264.0	37431824.0	GSM2700309 r1	0:61	A:647837199;C:525057060;G:652558979;T:457828691;N:59335	61		647837199	525057060	652558979	457828691	59335	SRX2996176	SRS2347410	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.51394		0.14658		0.85125		0.68998		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42881	42881	SRR5817921	SRX2996175	SRS2347411	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343	postnb citrine 7dpi 07	GSM2700308	tissue:Heart\|cell type:postnb:citrine+\|treatment:7 xxx post injury\|pool:7	postnb citrine 7dpi 07	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:postnb:citrine+\|treatment:7 xxx post injury\|pool:7	GSM2700308	GSM2700308: postnb citrine 7dpi 07; Danio rerio; RNA Seq	GSM2700308		1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700308	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552	postnb_7dpi_07__HS_OvationSC_GAGTCA_L008_R1_001.fastq.gz	fastq	722584040.0	11845640.0	GSM2700308 r1	0:61	A:200442958;C:161168985;G:204893226;T:156067063;N:11808	61		200442958	161168985	204893226	156067063	11808	SRX2996175	SRS2347411	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.50737		0.15544		0.85719		0.49067		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42882	42882	SRR5817920	SRX2996174	SRS2347409	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343	kdrl mCherry 7dpi 09	GSM2700307	tissue:Heart\|cell type:kdrl:mCherry+\|treatment:7 xxx post injury\|pool:9	kdrl mCherry 7dpi 09	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:kdrl:mCherry+\|treatment:7 xxx post injury\|pool:9	GSM2700307	GSM2700307: kdrl mCherry 7dpi 09; Danio rerio; RNA Seq	GSM2700307		1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700307	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552	kdrl_7dpi_09__HS_OvationSC_TGGTGA_L001_R1_001.fastq.gz	fastq	2145360789.0	35169849.0	GSM2700307 r1	0:61	A:559652295;C:434757157;G:629761603;T:521131593;N:58141	61		559652295	434757157	629761603	521131593	58141	SRX2996174	SRS2347409	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.76139		0.25919		0.80608		0.67486		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42883	42883	SRR5817919	SRX2996173	SRS2347408	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343	kdrl mCherry 7dpi 07	GSM2700306	tissue:Heart\|cell type:kdrl:mCherry+\|treatment:7 xxx post injury\|pool:7	kdrl mCherry 7dpi 07	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:kdrl:mCherry+\|treatment:7 xxx post injury\|pool:7	GSM2700306	GSM2700306: kdrl mCherry 7dpi 07; Danio rerio; RNA Seq	GSM2700306		1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700306	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552	kdrl_7dpi_07__HS_OvationSC_CGTAGA_L008_R1_001.fastq.gz	fastq	803488645.0	13171945.0	GSM2700306 r1	0:61	A:219205587;C:172957534;G:230065287;T:181248332;N:11905	61		219205587	172957534	230065287	181248332	11905	SRX2996173	SRS2347408	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.61434		0.19945		0.85242		0.62325		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42884	42884	SRR5817918	SRX2996172	SRS2347407	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343	kdrl mCherry 7dpi 06	GSM2700305	tissue:Heart\|cell type:kdrl:mCherry+\|treatment:7 xxx post injury\|pool:6	kdrl mCherry 7dpi 06	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:kdrl:mCherry+\|treatment:7 xxx post injury\|pool:6	GSM2700305	GSM2700305: kdrl mCherry 7dpi 06; Danio rerio; RNA Seq	GSM2700305		1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700305	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552	kdrl_7dpi_06__HS_OvationSC_GGAGAA_L008_R1_001.fastq.gz	fastq	720805646.0	11816486.0	GSM2700305 r1	0:61	A:200358132;C:158104743;G:199543761;T:162788231;N:10779	61		200358132	158104743	199543761	162788231	10779	SRX2996172	SRS2347407	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.45356		0.17003		0.85137		0.56525		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42885	42885	SRR5817917	SRX2996171	SRS2347406	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343	kdrl mCherry 7dpi 05	GSM2700304	tissue:Heart\|cell type:kdrl:mCherry+\|treatment:7 xxx post injury\|pool:5	kdrl mCherry 7dpi 05	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:kdrl:mCherry+\|treatment:7 xxx post injury\|pool:5	GSM2700304	GSM2700304: kdrl mCherry 7dpi 05; Danio rerio; RNA Seq	GSM2700304		1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700304	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552	kdrl_7dpi_05__HS_OvationSC_AAGCCT_L007_R1_001.fastq.gz	fastq	1380653870.0	22633670.0	GSM2700304 r1	0:61	A:388484121;C:311044648;G:367785851;T:313097333;N:241917	61		388484121	311044648	367785851	313097333	241917	SRX2996171	SRS2347406	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.44514		0.18589		0.85569		0.53637		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42886	42886	SRR5817916	SRX2996170	SRS2347405	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343	kdrl mCherry uninjured 04	GSM2700303	tissue:Heart\|cell type:kdrl:mCherry+\|treatment:Uninjured\|pool:4	kdrl mCherry uninjured 04	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:kdrl:mCherry+\|treatment:Uninjured\|pool:4	GSM2700303	GSM2700303: kdrl mCherry uninjured 04; Danio rerio; RNA Seq	GSM2700303		1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700303	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552	kdrl_uninj_04__HS_OvationSC_GCACTA_L007_R1_001.fastq.gz	fastq	1540717199.0	25257659.0	GSM2700303 r1	0:61	A:419376382;C:337803904;G:429107804;T:354151511;N:277598	61		419376382	337803904	429107804	354151511	277598	SRX2996170	SRS2347405	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.5821		0.21016		0.84904		0.6021		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42887	42887	SRR5817915	SRX2996169	SRS2347404	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343	kdrl mCherry uninjured 03	GSM2700302	tissue:Heart\|cell type:kdrl:mCherry+\|treatment:Uninjured\|pool:3	kdrl mCherry uninjured 03	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:kdrl:mCherry+\|treatment:Uninjured\|pool:3	GSM2700302	GSM2700302: kdrl mCherry uninjured 03; Danio rerio; RNA Seq	GSM2700302		1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700302	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552	kdrl_uninj_03__HS_OvationSC_AGTGAG_L007_R1_001.fastq.gz	fastq	1258645879.0	20633539.0	GSM2700302 r1	0:61	A:349212875;C:258591407;G:348719714;T:301896773;N:225110	61		349212875	258591407	348719714	301896773	225110	SRX2996169	SRS2347404	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.59499		0.22916		0.83508		0.54761		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42888	42888	SRR5817914	SRX2996168	SRS2347403	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343	kdrl mCherry uninjured 02	GSM2700301	tissue:Heart\|cell type:kdrl:mCherry+\|treatment:Uninjured\|pool:2	kdrl mCherry uninjured 02	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:kdrl:mCherry+\|treatment:Uninjured\|pool:2	GSM2700301	GSM2700301: kdrl mCherry uninjured 02; Danio rerio; RNA Seq	GSM2700301		1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700301	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552	kdrl_uninj_02__HS_OvationSC_TGGTGA_L007_R1_001.fastq.gz	fastq	1339434096.0	21957936.0	GSM2700301 r1	0:61	A:368699684;C:287536628;G:376256631;T:306701372;N:239781	61		368699684	287536628	376256631	306701372	239781	SRX2996168	SRS2347403	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.41301		0.17019		0.85458		0.5146		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42889	42889	SRR5818018	SRX2996265	SRS2347497	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343	wt1aGFP 4 pos	GSM2700333	tissue:Heart\|cell type:wt1a+\|pool:4	wt1aGFP 4 pos	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a+\|pool:4	GSM2700333	GSM2700333: wt1aGFP 4 pos; Danio rerio; RNA Seq	GSM2700333		1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700333	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553	wt1aV_34_pos__HS_RNA_Seq_OvationSC_GTCGTA_L001_R1_001.fastq.gz	fastq	723314759.0	11857619.0	GSM2700333 r1	0:61	A:201917485;C:141523845;G:184676365;T:195150579;N:46485	61		201917485	141523845	184676365	195150579	46485	SRX2996265	SRS2347497	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.82231		0.30947		0.80137		0.55406		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42890	42890	SRR5818019	SRX2996265	SRS2347497	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343	wt1aGFP 4 pos	GSM2700333	tissue:Heart\|cell type:wt1a+\|pool:4	wt1aGFP 4 pos	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a+\|pool:4	GSM2700333	GSM2700333: wt1aGFP 4 pos; Danio rerio; RNA Seq	GSM2700333		1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700333	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553	wt1aV_34_pos__HS_RNA_Seq_OvationSC_GTCGTA_L002_R1_001.fastq.gz	fastq	736427807.0	12072587.0	GSM2700333 r2	0:61	A:205663718;C:144074430;G:188007794;T:198654037;N:27828	61		205663718	144074430	188007794	198654037	27828	SRX2996265	SRS2347497	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.82156		0.3081		0.80107		0.55258		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42891	42891	SRR5818016	SRX2996264	SRS2347496	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343	wt1aGFP 4 neg	GSM2700332	tissue:Heart\|cell type:wt1a \|pool:4	wt1aGFP 4 neg	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a \|pool:4	GSM2700332	GSM2700332: wt1aGFP 4 neg; Danio rerio; RNA Seq	GSM2700332		1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700332	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553	wt1aV_34_neg__HS_RNA_Seq_OvationSC_AAGCCT_L001_R1_001.fastq.gz	fastq	845878277.0	13866857.0	GSM2700332 r1	0:61	A:249667621;C:171998644;G:210584175;T:213573132;N:54705	61		249667621	171998644	210584175	213573132	54705	SRX2996264	SRS2347496	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.90245		0.18824		0.81793		0.69585		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42892	42892	SRR5818017	SRX2996264	SRS2347496	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343	wt1aGFP 4 neg	GSM2700332	tissue:Heart\|cell type:wt1a \|pool:4	wt1aGFP 4 neg	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a \|pool:4	GSM2700332	GSM2700332: wt1aGFP 4 neg; Danio rerio; RNA Seq	GSM2700332		1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700332	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553	wt1aV_34_neg__HS_RNA_Seq_OvationSC_AAGCCT_L002_R1_001.fastq.gz	fastq	862736664.0	14143224.0	GSM2700332 r2	0:61	A:254822084;C:175437676;G:214663386;T:217781386;N:32132	61		254822084	175437676	214663386	217781386	32132	SRX2996264	SRS2347496	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.90087		0.1871		0.81779		0.68372		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42893	42893	SRR5818014	SRX2996263	SRS2347495	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343	wt1aGFP 3 pos	GSM2700331	tissue:Heart\|cell type:wt1a+\|pool:3	wt1aGFP 3 pos	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a+\|pool:3	GSM2700331	GSM2700331: wt1aGFP 3 pos; Danio rerio; RNA Seq	GSM2700331		1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700331	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553	wt1aV_33_pos__HS_RNA_Seq_OvationSC_GTGCTT_L001_R1_001.fastq.gz	fastq	774308441.0	12693581.0	GSM2700331 r1	0:61	A:214992220;C:150401431;G:203530010;T:205334623;N:50157	61		214992220	150401431	203530010	205334623	50157	SRX2996263	SRS2347495	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.85135		0.30434		0.79859		0.56227		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42894	42894	SRR5818015	SRX2996263	SRS2347495	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343	wt1aGFP 3 pos	GSM2700331	tissue:Heart\|cell type:wt1a+\|pool:3	wt1aGFP 3 pos	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a+\|pool:3	GSM2700331	GSM2700331: wt1aGFP 3 pos; Danio rerio; RNA Seq	GSM2700331		1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700331	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553	wt1aV_33_pos__HS_RNA_Seq_OvationSC_GTGCTT_L002_R1_001.fastq.gz	fastq	785516154.0	12877314.0	GSM2700331 r2	0:61	A:218236052;C:152511901;G:206411606;T:208326427;N:30168	61		218236052	152511901	206411606	208326427	30168	SRX2996263	SRS2347495	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.85177		0.30473		0.80081		0.56348		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42895	42895	SRR5818012	SRX2996262	SRS2347494	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343	wt1aGFP 3 neg	GSM2700330	tissue:Heart\|cell type:wt1a \|pool:3	wt1aGFP 3 neg	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a \|pool:3	GSM2700330	GSM2700330: wt1aGFP 3 neg; Danio rerio; RNA Seq	GSM2700330		1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700330	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553	wt1aV_33_neg__HS_RNA_Seq_OvationSC_ACCTCA_L001_R1_001.fastq.gz	fastq	725733470.0	11897270.0	GSM2700330 r1	0:61	A:216602034;C:144864671;G:177825033;T:186394034;N:47698	61		216602034	144864671	177825033	186394034	47698	SRX2996262	SRS2347494	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.89906		0.20936		0.81264		0.69072		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42896	42896	SRR5818013	SRX2996262	SRS2347494	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343	wt1aGFP 3 neg	GSM2700330	tissue:Heart\|cell type:wt1a \|pool:3	wt1aGFP 3 neg	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a \|pool:3	GSM2700330	GSM2700330: wt1aGFP 3 neg; Danio rerio; RNA Seq	GSM2700330		1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700330	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553	wt1aV_33_neg__HS_RNA_Seq_OvationSC_ACCTCA_L002_R1_001.fastq.gz	fastq	739526485.0	12123385.0	GSM2700330 r2	0:61	A:220804426;C:147618040;G:181199008;T:189877408;N:27603	61		220804426	147618040	181199008	189877408	27603	SRX2996262	SRS2347494	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.89897		0.20803		0.8126		0.68941		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42897	42897	SRR5818010	SRX2996261	SRS2347493	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343	wt1aGFP 2 pos	GSM2700329	tissue:Heart\|cell type:wt1a+\|pool:2	wt1aGFP 2 pos	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a+\|pool:2	GSM2700329	GSM2700329: wt1aGFP 2 pos; Danio rerio; RNA Seq	GSM2700329		1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700329	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553	wt1aV_32_pos__HS_RNA_Seq_OvationSC_GCACTA_L001_R1_001.fastq.gz	fastq	754469960.0	12368360.0	GSM2700329 r1	0:61	A:212826941;C:144472909;G:187613892;T:209506276;N:49942	61		212826941	144472909	187613892	209506276	49942	SRX2996261	SRS2347493	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.82785		0.31821		0.79113		0.57087		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42898	42898	SRR5818011	SRX2996261	SRS2347493	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343	wt1aGFP 2 pos	GSM2700329	tissue:Heart\|cell type:wt1a+\|pool:2	wt1aGFP 2 pos	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a+\|pool:2	GSM2700329	GSM2700329: wt1aGFP 2 pos; Danio rerio; RNA Seq	GSM2700329		1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700329	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553	wt1aV_32_pos__HS_RNA_Seq_OvationSC_GCACTA_L002_R1_001.fastq.gz	fastq	768777327.0	12602907.0	GSM2700329 r2	0:61	A:216934227;C:147173989;G:191157153;T:213483110;N:28848	61		216934227	147173989	191157153	213483110	28848	SRX2996261	SRS2347493	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.82552		0.31671		0.79088		0.50918		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42899	42899	SRR5818008	SRX2996260	SRS2347491	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343	wt1aGFP 2 neg	GSM2700328	tissue:Heart\|cell type:wt1a \|pool:2	wt1aGFP 2 neg	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a \|pool:2	GSM2700328	GSM2700328: wt1aGFP 2 neg; Danio rerio; RNA Seq	GSM2700328		1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700328	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553	wt1aV_32_neg__HS_RNA_Seq_OvationSC_AGTGAG_L001_R1_001.fastq.gz	fastq	692638530.0	11354730.0	GSM2700328 r1	0:61	A:211149267;C:142433123;G:165634275;T:173375719;N:46146	61		211149267	142433123	165634275	173375719	46146	SRX2996260	SRS2347491	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.91099		0.17805		0.81458		0.72923		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42900	42900	SRR5818009	SRX2996260	SRS2347491	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343	wt1aGFP 2 neg	GSM2700328	tissue:Heart\|cell type:wt1a \|pool:2	wt1aGFP 2 neg	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a \|pool:2	GSM2700328	GSM2700328: wt1aGFP 2 neg; Danio rerio; RNA Seq	GSM2700328		1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700328	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553	wt1aV_32_neg__HS_RNA_Seq_OvationSC_AGTGAG_L002_R1_001.fastq.gz	fastq	704040406.0	11541646.0	GSM2700328 r2	0:61	A:214725213;C:144725366;G:168345724;T:176217859;N:26244	61		214725213	144725366	168345724	176217859	26244	SRX2996260	SRS2347491	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.90997		0.17763		0.81527		0.72316		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42901	42901	SRR5818006	SRX2996259	SRS2347492	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343	wt1aGFP 1 pos	GSM2700327	tissue:Heart\|cell type:wt1a+\|pool:1	wt1aGFP 1 pos	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a+\|pool:1	GSM2700327	GSM2700327: wt1aGFP 1 pos; Danio rerio; RNA Seq	GSM2700327		1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700327	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553	wt1aV_31_pos__HS_RNA_Seq_OvationSC_TGGTGA_L001_R1_001.fastq.gz	fastq	729643509.0	11961369.0	GSM2700327 r1	0:61	A:209109414;C:140044116;G:176769088;T:203672961;N:47930	61		209109414	140044116	176769088	203672961	47930	SRX2996259	SRS2347492	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.82015		0.30797		0.79748		0.46884		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42902	42902	SRR5818007	SRX2996259	SRS2347492	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343	wt1aGFP 1 pos	GSM2700327	tissue:Heart\|cell type:wt1a+\|pool:1	wt1aGFP 1 pos	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a+\|pool:1	GSM2700327	GSM2700327: wt1aGFP 1 pos; Danio rerio; RNA Seq	GSM2700327		1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700327	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553	wt1aV_31_pos__HS_RNA_Seq_OvationSC_TGGTGA_L002_R1_001.fastq.gz	fastq	743468183.0	12188003.0	GSM2700327 r2	0:61	A:213138374;C:142664132;G:180105124;T:207532889;N:27664	61		213138374	142664132	180105124	207532889	27664	SRX2996259	SRS2347492	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.81957		0.30392		0.79527		0.47293		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42903	42903	SRR5818004	SRX2996258	SRS2347490	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343	wt1aGFP 1 neg	GSM2700326	tissue:Heart\|cell type:wt1a \|pool:1	wt1aGFP 1 neg	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a \|pool:1	GSM2700326	GSM2700326: wt1aGFP 1 neg; Danio rerio; RNA Seq	GSM2700326		1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700326	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553	wt1aV_31_neg__HS_RNA_Seq_OvationSC_AACCAG_L001_R1_001.fastq.gz	fastq	830080436.0	13607876.0	GSM2700326 r1	0:61	A:251391883;C:167411203;G:203106619;T:208117027;N:53704	61		251391883	167411203	203106619	208117027	53704	SRX2996258	SRS2347490	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.88568		0.18069		0.82298		0.729		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42904	42904	SRR5818005	SRX2996258	SRS2347490	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343	wt1aGFP 1 neg	GSM2700326	tissue:Heart\|cell type:wt1a \|pool:1	wt1aGFP 1 neg	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a \|pool:1	GSM2700326	GSM2700326: wt1aGFP 1 neg; Danio rerio; RNA Seq	GSM2700326		1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700326	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553	wt1aV_31_neg__HS_RNA_Seq_OvationSC_AACCAG_L002_R1_001.fastq.gz	fastq	841688675.0	13798175.0	GSM2700326 r2	0:61	A:255002009;C:169696986;G:205887037;T:211071121;N:31522	61		255002009	169696986	205887037	211071121	31522	SRX2996258	SRS2347490	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.88535		0.18061		0.82199		0.73203		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42905	42905	SRR5820065	SRX2997963	SRS2349071	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343	postnbCreERT2 60dpi 4	GSM2700300	tissue:Heart\|treatment:60 dpi	postnbCreERT2 60dpi 4	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:60 dpi	GSM2700300	GSM2700300: postnbCreERT2 60dpi 4; Danio rerio; RNA Seq	GSM2700300		1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700300	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705	pstnC60dpi_24__HS_RNA_Seq_OvationSC_TTGGCA_L001_R1_001.fastq.gz	fastq	658472125.0	10794625.0	GSM2700300 r1										SRX2997963	SRS2349071	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.81414		0.33277		0.81746		0.52723		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42906	42906	SRR5820066	SRX2997963	SRS2349071	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343	postnbCreERT2 60dpi 4	GSM2700300	tissue:Heart\|treatment:60 dpi	postnbCreERT2 60dpi 4	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:60 dpi	GSM2700300	GSM2700300: postnbCreERT2 60dpi 4; Danio rerio; RNA Seq	GSM2700300		1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700300	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705	pstnC60dpi_24__HS_RNA_Seq_OvationSC_TTGGCA_L002_R1_001.fastq.gz	fastq	667651710.0	10945110.0	GSM2700300 r2	0:61	A:187398827;C:124387075;G:170371629;T:185469418;N:24761	61		187398827	124387075	170371629	185469418	24761	SRX2997963	SRS2349071	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.81012		0.32665		0.82207		0.52786		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42907	42907	SRR5820063	SRX2997962	SRS2349070	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343	postnbCreERT2 60dpi 2	GSM2700299	tissue:Heart\|treatment:60 dpi	postnbCreERT2 60dpi 2	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:60 dpi	GSM2700299	GSM2700299: postnbCreERT2 60dpi 2; Danio rerio; RNA Seq	GSM2700299		1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700299	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705	pstnC60dpi_22__HS_RNA_Seq_OvationSC_TCAGAG_L001_R1_001.fastq.gz	fastq	812209022.0	13314902.0	GSM2700299 r1	0:61	A:228658409;C:151594988;G:205412898;T:226488086;N:54641	61		228658409	151594988	205412898	226488086	54641	SRX2997962	SRS2349070	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.84081		0.33669		0.80026		0.55189		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42908	42908	SRR5820064	SRX2997962	SRS2349070	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343	postnbCreERT2 60dpi 2	GSM2700299	tissue:Heart\|treatment:60 dpi	postnbCreERT2 60dpi 2	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:60 dpi	GSM2700299	GSM2700299: postnbCreERT2 60dpi 2; Danio rerio; RNA Seq	GSM2700299		1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700299	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705	pstnC60dpi_22__HS_RNA_Seq_OvationSC_TCAGAG_L002_R1_001.fastq.gz	fastq	824141232.0	13510512.0	GSM2700299 r2	0:61	A:232162664;C:153749805;G:208354200;T:229843231;N:31332	61		232162664	153749805	208354200	229843231	31332	SRX2997962	SRS2349070	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.83912		0.33627		0.79935		0.55638		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42909	42909	SRR5820061	SRX2997961	SRS2349069	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343	postnbCreERT2 60dpi 1	GSM2700298	tissue:Heart\|treatment:60 dpi	postnbCreERT2 60dpi 1	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:60 dpi	GSM2700298	GSM2700298: postnbCreERT2 60dpi 1; Danio rerio; RNA Seq	GSM2700298		1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700298	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705	pstnC60dpi_21__HS_RNA_Seq_OvationSC_CGTAGA_L001_R1_001.fastq.gz	fastq	820312811.0	13447751.0	GSM2700298 r1	0:61	A:224903496;C:155230235;G:218395518;T:221729453;N:54109	61		224903496	155230235	218395518	221729453	54109	SRX2997961	SRS2349069	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.82352		0.30266		0.7936		0.54956		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42910	42910	SRR5820062	SRX2997961	SRS2349069	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343	postnbCreERT2 60dpi 1	GSM2700298	tissue:Heart\|treatment:60 dpi	postnbCreERT2 60dpi 1	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:60 dpi	GSM2700298	GSM2700298: postnbCreERT2 60dpi 1; Danio rerio; RNA Seq	GSM2700298		1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700298	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705	pstnC60dpi_21__HS_RNA_Seq_OvationSC_CGTAGA_L002_R1_001.fastq.gz	fastq	831069612.0	13624092.0	GSM2700298 r2	0:61	A:227982894;C:157205567;G:221135004;T:224715301;N:30846	61		227982894	157205567	221135004	224715301	30846	SRX2997961	SRS2349069	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.82359		0.30223		0.79876		0.5386		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42911	42911	SRR5820059	SRX2997960	SRS2349068	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343	postnbCreERT2 7dpi 4	GSM2700297	tissue:Heart\|treatment:7 dpi	postnbCreERT2 7dpi 4	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:7 dpi	GSM2700297	GSM2700297: postnbCreERT2 7dpi 4; Danio rerio; RNA Seq	GSM2700297		1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700297	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705	pstnC7dpi_24__HS_RNA_Seq_OvationSC_GAGTCA_L001_R1_001.fastq.gz	fastq	529129067.0	8674247.0	GSM2700297 r1	0:61	A:145838822;C:101005915;G:133827073;T:148422408;N:34849	61		145838822	101005915	133827073	148422408	34849	SRX2997960	SRS2349068	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.85327		0.29887		0.82398		0.59536		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42912	42912	SRR5820060	SRX2997960	SRS2349068	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343	postnbCreERT2 7dpi 4	GSM2700297	tissue:Heart\|treatment:7 dpi	postnbCreERT2 7dpi 4	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:7 dpi	GSM2700297	GSM2700297: postnbCreERT2 7dpi 4; Danio rerio; RNA Seq	GSM2700297		1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700297	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705	pstnC7dpi_24__HS_RNA_Seq_OvationSC_GAGTCA_L002_R1_001.fastq.gz	fastq	537096033.0	8804853.0	GSM2700297 r2	0:61	A:148103577;C:102498850;G:135735762;T:150738056;N:19788	61		148103577	102498850	135735762	150738056	19788	SRX2997960	SRS2349068	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.85107		0.29724		0.82489		0.59155		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42913	42913	SRR5820057	SRX2997959	SRS2349067	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343	postnbCreERT2 7dpi 3	GSM2700296	tissue:Heart\|treatment:7 dpi	postnbCreERT2 7dpi 3	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:7 dpi	GSM2700296	GSM2700296: postnbCreERT2 7dpi 3; Danio rerio; RNA Seq	GSM2700296		1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700296	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705	pstnC7dpi_23__HS_RNA_Seq_OvationSC_AGCATG_L001_R1_001.fastq.gz	fastq	732770857.0	12012637.0	GSM2700296 r1	0:61	A:202857149;C:140357985;G:191010203;T:198497101;N:48419	61		202857149	140357985	191010203	198497101	48419	SRX2997959	SRS2349067	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.84025		0.28858		0.78297		0.58582		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42914	42914	SRR5820058	SRX2997959	SRS2349067	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343	postnbCreERT2 7dpi 3	GSM2700296	tissue:Heart\|treatment:7 dpi	postnbCreERT2 7dpi 3	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:7 dpi	GSM2700296	GSM2700296: postnbCreERT2 7dpi 3; Danio rerio; RNA Seq	GSM2700296		1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700296	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705	pstnC7dpi_23__HS_RNA_Seq_OvationSC_AGCATG_L002_R1_001.fastq.gz	fastq	742926320.0	12179120.0	GSM2700296 r2	0:61	A:205824167;C:142245364;G:193518156;T:201311005;N:27628	61		205824167	142245364	193518156	201311005	27628	SRX2997959	SRS2349067	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.83963		0.28878		0.78577		0.57339		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42915	42915	SRR5820055	SRX2997958	SRS2349066	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343	postnbCreERT2 7dpi 2	GSM2700295	tissue:Heart\|treatment:7 dpi	postnbCreERT2 7dpi 2	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:7 dpi	GSM2700295	GSM2700295: postnbCreERT2 7dpi 2; Danio rerio; RNA Seq	GSM2700295		1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700295	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705	pstnC7dpi_22__HS_RNA_Seq_OvationSC_GGAGAA_L001_R1_001.fastq.gz	fastq	798125708.0	13084028.0	GSM2700295 r1	0:61	A:220033386;C:154219970;G:209254999;T:214564836;N:52517	61		220033386	154219970	209254999	214564836	52517	SRX2997958	SRS2349066	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.84868		0.29566		0.78395		0.60892		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42916	42916	SRR5820056	SRX2997958	SRS2349066	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343	postnbCreERT2 7dpi 2	GSM2700295	tissue:Heart\|treatment:7 dpi	postnbCreERT2 7dpi 2	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:7 dpi	GSM2700295	GSM2700295: postnbCreERT2 7dpi 2; Danio rerio; RNA Seq	GSM2700295		1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700295	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705	pstnC7dpi_22__HS_RNA_Seq_OvationSC_GGAGAA_L002_R1_001.fastq.gz	fastq	811023060.0	13295460.0	GSM2700295 r2	0:61	A:223729714;C:156680800;G:212510056;T:218071242;N:31248	61		223729714	156680800	212510056	218071242	31248	SRX2997958	SRS2349066	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.85147		0.29531		0.78614		0.59452		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42917	42917	SRR5820053	SRX2997957	SRS2349065	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343	postnbCreERT2 7dpi 1	GSM2700294	tissue:Heart\|treatment:7 dpi	postnbCreERT2 7dpi 1	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:7 dpi	GSM2700294	GSM2700294: postnbCreERT2 7dpi 1; Danio rerio; RNA Seq	GSM2700294		1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700294	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705	pstnC7dpi_21__HS_RNA_Seq_OvationSC_AAGAGG_L001_R1_001.fastq.gz	fastq	791727113.0	12979133.0	GSM2700294 r1	0:61	A:221474690;C:149322441;G:203129939;T:217747332;N:52711	61		221474690	149322441	203129939	217747332	52711	SRX2997957	SRS2349065	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.82196		0.30812		0.7895		0.58101		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42918	42918	SRR5820054	SRX2997957	SRS2349065	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343	postnbCreERT2 7dpi 1	GSM2700294	tissue:Heart\|treatment:7 dpi	postnbCreERT2 7dpi 1	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:7 dpi	GSM2700294	GSM2700294: postnbCreERT2 7dpi 1; Danio rerio; RNA Seq	GSM2700294		1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700294	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705	pstnC7dpi_21__HS_RNA_Seq_OvationSC_AAGAGG_L002_R1_001.fastq.gz	fastq	801987435.0	13147335.0	GSM2700294 r2	0:61	A:224436021;C:151157500;G:205611822;T:220752212;N:29880	61		224436021	151157500	205611822	220752212	29880	SRX2997957	SRS2349065	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.82242		0.30689		0.79044		0.57309		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
48425	48425	SRR7266726	SRX4170565	SRS3382375	SRP149832	PRJNA474730	Transcriptome analysis of wt1b:eGFP positive macrophages in the regenerating zebrafish heart	GSE115381	Transcriptome Analysis	Little is known about zebrafish macrophage subtypes and their contribution to organ regeneration. Using the transgenic line wt1b:eGFP we identified a subtype of macrophages in the regenerating heart that is transcriptionally different from the rest of macrophages. Overall design: Hearts from Tgwt1b:eGFP; mpeg1:mCherry zebrafish were cryoinjured and at 4 dpi mCherry and GFP/mCherry cells were FAC sorted. RNA was extracted from 4 pools of GFP/mCherry and 4 pools of mCherry single positive cells and RNAseq was performed.	parent bioproject:PRJNA485878	pubmed:31365871	MRWT1 5	GSM3177088	tissue:mpeg1:mCherry/wt1b:eGFP cells from 4dpi hearts\|phenotype:mpeg1:mCherry/wt1b:eGFP\|library batch:2	MRWT1 5	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM normalized batch corrected counts per million for each sample.	mpeg1:mCherry/wt1b:eGFP cells from 4dpi hearts	Four biological replicates consisting of FAC sorted cells coming from five to seven pooled hearts were used per phenotype.	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	phenotype:mpeg1:mCherry/wt1b:eGFP\|library batch:2	GSM3177088	GSM3177088: MRWT1 5; Danio rerio; RNA Seq	GSM3177088		1	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	GEO Accession:GSM3177088	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP149832	MRWT15__AnaBelenGarcia_RNA_Seq_OvationSC_GAGTCA_L002_R1_001.fastq.gz	fastq	1609149012.0	26379492.0	GSM3177088 r1	0:61 1:0	A:432557422;C:346615764;G:438332984;T:391553708;N:89134	61	0	432557422	346615764	438332984	391553708	89134	SRX4170565	SRS3382375	SRA715602	GEO	Bioinformatics Unit, CNIC	1	0.75712		0.25964		0.83737		0.58775		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2018-06-05	Adult	Adult	Heart	Cardiovascular System
48426	48426	SRR7266725	SRX4170564	SRS3382374	SRP149832	PRJNA474730	Transcriptome analysis of wt1b:eGFP positive macrophages in the regenerating zebrafish heart	GSE115381	Transcriptome Analysis	Little is known about zebrafish macrophage subtypes and their contribution to organ regeneration. Using the transgenic line wt1b:eGFP we identified a subtype of macrophages in the regenerating heart that is transcriptionally different from the rest of macrophages. Overall design: Hearts from Tgwt1b:eGFP; mpeg1:mCherry zebrafish were cryoinjured and at 4 dpi mCherry and GFP/mCherry cells were FAC sorted. RNA was extracted from 4 pools of GFP/mCherry and 4 pools of mCherry single positive cells and RNAseq was performed.	parent bioproject:PRJNA485878	pubmed:31365871	MRWT1 4	GSM3177087	tissue:mpeg1:mCherry/wt1b:eGFP cells from 4dpi hearts\|phenotype:mpeg1:mCherry/wt1b:eGFP\|library batch:2	MRWT1 4	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM normalized batch corrected counts per million for each sample.	mpeg1:mCherry/wt1b:eGFP cells from 4dpi hearts	Four biological replicates consisting of FAC sorted cells coming from five to seven pooled hearts were used per phenotype.	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	phenotype:mpeg1:mCherry/wt1b:eGFP\|library batch:2	GSM3177087	GSM3177087: MRWT1 4; Danio rerio; RNA Seq	GSM3177087		1	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	GEO Accession:GSM3177087	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP149832	MRWT14__AnaBelenGarcia_RNA_Seq_OvationSC_AGCATG_L002_R1_001.fastq.gz	fastq	1578335899.0	25874359.0	GSM3177087 r1	0:61 1:0	A:403622771;C:331438424;G:444808774;T:398377182;N:88748	61	0	403622771	331438424	444808774	398377182	88748	SRX4170564	SRS3382374	SRA715602	GEO	Bioinformatics Unit, CNIC	1	0.87043		0.29681		0.84376		0.60111		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2018-06-05	Adult	Adult	Heart	Cardiovascular System
48427	48427	SRR7266724	SRX4170563	SRS3382372	SRP149832	PRJNA474730	Transcriptome analysis of wt1b:eGFP positive macrophages in the regenerating zebrafish heart	GSE115381	Transcriptome Analysis	Little is known about zebrafish macrophage subtypes and their contribution to organ regeneration. Using the transgenic line wt1b:eGFP we identified a subtype of macrophages in the regenerating heart that is transcriptionally different from the rest of macrophages. Overall design: Hearts from Tgwt1b:eGFP; mpeg1:mCherry zebrafish were cryoinjured and at 4 dpi mCherry and GFP/mCherry cells were FAC sorted. RNA was extracted from 4 pools of GFP/mCherry and 4 pools of mCherry single positive cells and RNAseq was performed.	parent bioproject:PRJNA485878	pubmed:31365871	MRWT1 2	GSM3177086	tissue:mpeg1:mCherry/wt1b:eGFP cells from 4dpi hearts\|phenotype:mpeg1:mCherry/wt1b:eGFP\|library batch:1	MRWT1 2	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM normalized batch corrected counts per million for each sample.	mpeg1:mCherry/wt1b:eGFP cells from 4dpi hearts	Four biological replicates consisting of FAC sorted cells coming from five to seven pooled hearts were used per phenotype.	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	phenotype:mpeg1:mCherry/wt1b:eGFP\|library batch:1	GSM3177086	GSM3177086: MRWT1 2; Danio rerio; RNA Seq	GSM3177086		1	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	GEO Accession:GSM3177086	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP149832	MRWT1_2__AnaBelenGarcia_RNA_Seq_OvationSC_CACAGT_L001_R1_001.fastq.gz	fastq	1647958920.0	27465982.0	GSM3177086 r1	0:60	A:443708613;C:313933032;G:445835945;T:444367644;N:113686	60		443708613	313933032	445835945	444367644	113686	SRX4170563	SRS3382372	SRA715602	GEO	Bioinformatics Unit, CNIC	1	0.85143		0.29582		0.83564		0.59274		60		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2018-06-05	Adult	Adult	Heart	Cardiovascular System
48428	48428	SRR7266723	SRX4170562	SRS3382373	SRP149832	PRJNA474730	Transcriptome analysis of wt1b:eGFP positive macrophages in the regenerating zebrafish heart	GSE115381	Transcriptome Analysis	Little is known about zebrafish macrophage subtypes and their contribution to organ regeneration. Using the transgenic line wt1b:eGFP we identified a subtype of macrophages in the regenerating heart that is transcriptionally different from the rest of macrophages. Overall design: Hearts from Tgwt1b:eGFP; mpeg1:mCherry zebrafish were cryoinjured and at 4 dpi mCherry and GFP/mCherry cells were FAC sorted. RNA was extracted from 4 pools of GFP/mCherry and 4 pools of mCherry single positive cells and RNAseq was performed.	parent bioproject:PRJNA485878	pubmed:31365871	MRWT1 1	GSM3177085	tissue:mpeg1:mCherry/wt1b:eGFP cells from 4dpi hearts\|phenotype:mpeg1:mCherry/wt1b:eGFP\|library batch:1	MRWT1 1	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM normalized batch corrected counts per million for each sample.	mpeg1:mCherry/wt1b:eGFP cells from 4dpi hearts	Four biological replicates consisting of FAC sorted cells coming from five to seven pooled hearts were used per phenotype.	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	phenotype:mpeg1:mCherry/wt1b:eGFP\|library batch:1	GSM3177085	GSM3177085: MRWT1 1; Danio rerio; RNA Seq	GSM3177085		1	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	GEO Accession:GSM3177085	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP149832	MRWT1_1__AnaBelenGarcia_RNA_Seq_OvationSC_TCAGAG_L001_R1_001.fastq.gz	fastq	1361787360.0	22696456.0	GSM3177085 r1	0:60	A:365235306;C:266923973;G:370787525;T:358747902;N:92654	60		365235306	266923973	370787525	358747902	92654	SRX4170562	SRS3382373	SRA715602	GEO	Bioinformatics Unit, CNIC	1	0.79693		0.28628		0.87903		0.55995		60		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2018-06-05	Adult	Adult	Heart	Cardiovascular System
48429	48429	SRR7266722	SRX4170561	SRS3382371	SRP149832	PRJNA474730	Transcriptome analysis of wt1b:eGFP positive macrophages in the regenerating zebrafish heart	GSE115381	Transcriptome Analysis	Little is known about zebrafish macrophage subtypes and their contribution to organ regeneration. Using the transgenic line wt1b:eGFP we identified a subtype of macrophages in the regenerating heart that is transcriptionally different from the rest of macrophages. Overall design: Hearts from Tgwt1b:eGFP; mpeg1:mCherry zebrafish were cryoinjured and at 4 dpi mCherry and GFP/mCherry cells were FAC sorted. RNA was extracted from 4 pools of GFP/mCherry and 4 pools of mCherry single positive cells and RNAseq was performed.	parent bioproject:PRJNA485878	pubmed:31365871	MR 5	GSM3177084	tissue:mpeg1:mCherry cells from 4dpi hearts\|phenotype:mpeg1:mCherry\|library batch:2	MR 5	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM normalized batch corrected counts per million for each sample.	mpeg1:mCherry cells from 4dpi hearts	Four biological replicates consisting of FAC sorted cells coming from five to seven pooled hearts were used per phenotype.	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	phenotype:mpeg1:mCherry\|library batch:2	GSM3177084	GSM3177084: MR 5; Danio rerio; RNA Seq	GSM3177084		1	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	GEO Accession:GSM3177084	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP149832	MR5__AnaBelenGarcia_RNA_Seq_OvationSC_GGAGAA_L002_R1_001.fastq.gz	fastq	1159385276.0	19006316.0	GSM3177084 r1	0:61 1:0	A:316084223;C:249253761;G:317016302;T:276966251;N:64739	61	0	316084223	249253761	317016302	276966251	64739	SRX4170561	SRS3382371	SRA715602	GEO	Bioinformatics Unit, CNIC	1	0.72668		0.26774		0.84078		0.56426		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2018-06-05	Adult	Adult	Heart	Cardiovascular System
48430	48430	SRR7266721	SRX4170560	SRS3382369	SRP149832	PRJNA474730	Transcriptome analysis of wt1b:eGFP positive macrophages in the regenerating zebrafish heart	GSE115381	Transcriptome Analysis	Little is known about zebrafish macrophage subtypes and their contribution to organ regeneration. Using the transgenic line wt1b:eGFP we identified a subtype of macrophages in the regenerating heart that is transcriptionally different from the rest of macrophages. Overall design: Hearts from Tgwt1b:eGFP; mpeg1:mCherry zebrafish were cryoinjured and at 4 dpi mCherry and GFP/mCherry cells were FAC sorted. RNA was extracted from 4 pools of GFP/mCherry and 4 pools of mCherry single positive cells and RNAseq was performed.	parent bioproject:PRJNA485878	pubmed:31365871	MR 4	GSM3177083	tissue:mpeg1:mCherry cells from 4dpi hearts\|phenotype:mpeg1:mCherry\|library batch:2	MR 4	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM normalized batch corrected counts per million for each sample.	mpeg1:mCherry cells from 4dpi hearts	Four biological replicates consisting of FAC sorted cells coming from five to seven pooled hearts were used per phenotype.	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	phenotype:mpeg1:mCherry\|library batch:2	GSM3177083	GSM3177083: MR 4; Danio rerio; RNA Seq	GSM3177083		1	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	GEO Accession:GSM3177083	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP149832	MR4__AnaBelenGarcia_RNA_Seq_OvationSC_AAGAGG_L002_R1_001.fastq.gz	fastq	1031492188.0	16909708.0	GSM3177083 r1	0:61 1:0	A:275201446;C:215010611;G:277227531;T:263995484;N:57116	61	0	275201446	215010611	277227531	263995484	57116	SRX4170560	SRS3382369	SRA715602	GEO	Bioinformatics Unit, CNIC	1	0.8243		0.31617		0.83883		0.54481		61		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2018-06-05	Adult	Adult	Heart	Cardiovascular System
48431	48431	SRR7266720	SRX4170559	SRS3382370	SRP149832	PRJNA474730	Transcriptome analysis of wt1b:eGFP positive macrophages in the regenerating zebrafish heart	GSE115381	Transcriptome Analysis	Little is known about zebrafish macrophage subtypes and their contribution to organ regeneration. Using the transgenic line wt1b:eGFP we identified a subtype of macrophages in the regenerating heart that is transcriptionally different from the rest of macrophages. Overall design: Hearts from Tgwt1b:eGFP; mpeg1:mCherry zebrafish were cryoinjured and at 4 dpi mCherry and GFP/mCherry cells were FAC sorted. RNA was extracted from 4 pools of GFP/mCherry and 4 pools of mCherry single positive cells and RNAseq was performed.	parent bioproject:PRJNA485878	pubmed:31365871	MR 2	GSM3177082	tissue:mpeg1:mCherry cells from 4dpi hearts\|phenotype:mpeg1:mCherry\|library batch:1	MR 2	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM normalized batch corrected counts per million for each sample.	mpeg1:mCherry cells from 4dpi hearts	Four biological replicates consisting of FAC sorted cells coming from five to seven pooled hearts were used per phenotype.	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	phenotype:mpeg1:mCherry\|library batch:1	GSM3177082	GSM3177082: MR 2; Danio rerio; RNA Seq	GSM3177082		1	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	GEO Accession:GSM3177082	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP149832	MR2__AnaBelenGarcia_RNA_Seq_OvationSC_GAGTCA_L001_R1_001.fastq.gz	fastq	1423227000.0	23720450.0	GSM3177082 r1	0:60	A:409084360;C:294887211;G:360615674;T:358543749;N:96006	60		409084360	294887211	360615674	358543749	96006	SRX4170559	SRS3382370	SRA715602	GEO	Bioinformatics Unit, CNIC	1	0.65591		0.26043		0.82041		0.62336		60		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2018-06-05	Adult	Adult	Heart	Cardiovascular System
48432	48432	SRR7266719	SRX4170558	SRS3382368	SRP149832	PRJNA474730	Transcriptome analysis of wt1b:eGFP positive macrophages in the regenerating zebrafish heart	GSE115381	Transcriptome Analysis	Little is known about zebrafish macrophage subtypes and their contribution to organ regeneration. Using the transgenic line wt1b:eGFP we identified a subtype of macrophages in the regenerating heart that is transcriptionally different from the rest of macrophages. Overall design: Hearts from Tgwt1b:eGFP; mpeg1:mCherry zebrafish were cryoinjured and at 4 dpi mCherry and GFP/mCherry cells were FAC sorted. RNA was extracted from 4 pools of GFP/mCherry and 4 pools of mCherry single positive cells and RNAseq was performed.	parent bioproject:PRJNA485878	pubmed:31365871	MR 1	GSM3177081	tissue:mpeg1:mCherry cells from 4dpi hearts\|phenotype:mpeg1:mCherry\|library batch:1	MR 1	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM normalized batch corrected counts per million for each sample.	mpeg1:mCherry cells from 4dpi hearts	Four biological replicates consisting of FAC sorted cells coming from five to seven pooled hearts were used per phenotype.	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	phenotype:mpeg1:mCherry\|library batch:1	GSM3177081	GSM3177081: MR 1; Danio rerio; RNA Seq	GSM3177081		1	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	GEO Accession:GSM3177081	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP149832	MR1__AnaBelenGarcia_RNA_Seq_OvationSC_AGCATG_L001_R1_001.fastq.gz	fastq	1634874420.0	27247907.0	GSM3177081 r1	0:60	A:466410867;C:312698413;G:414814899;T:440838061;N:112180	60		466410867	312698413	414814899	440838061	112180	SRX4170558	SRS3382368	SRA715602	GEO	Bioinformatics Unit, CNIC	1	0.20756		0.07949		0.90019		0.64646		60		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2018-06-05	Adult	Adult	Heart	Cardiovascular System
66760	66760	SRR16573983	SRX12775941	SRS10721245	SRP343153	PRJNA774550	Single cell RNA sequencing of zebrafish hematopoietic stem cells and endothelial cells	GSE186565	Transcriptome Analysis	Assessing gene changes in endothelial to hematopoietic transition in control zebrafish embryos and comparing gene changes to those seen in vegfc knock down embryos. Overall design: 52 hpf embryos were dissociated for FACs sorting to isolate GFP+ HSPCs mCherry+ ECs and double positive cells undergoing EHT. Following the sort cells underwent standard 10x encapsulation.		pubmed:34919128	Vegfc MO	GSM5655701	tissue:Endothelial Cells HSPCs\|treatment:Vegfc MO\|strain:flk:mCherry; cd41:gfp\|age:52 hpf	Vegfc MO	Demultiplexing of raw base call files was done using cellranger mkfastq; version 4.0.0 Alignment filtering barcode counting and UMI counting was done using cellranger count; version 4.0.0 Samples were aggregated and normalized using cellranger aggr; version 4.0.0 Genome build: custom GRCz11 reporters Supplementary files format and content: Filtered feature barcode matrix	Endothelial Cells HSPCs	Control samples were not injected uninjected and treated samples were injected with 4 ng of vegfc MO at the one cell stage	Embryos were treated with a dissociation mix consisting of 480 ml 0.25% trypsin EDTA + 20 ml Collagenase 100 mg/ml for 15 mins at 30C. Once embryos were fully homogenized dissociation was stopped with addition of 800 ml of DMEM 10%FBS. The homogenate was run though a 70 uM strainer before centrifugation for 5 min at 700 g at room temperature. The pellet was resuspended in 1mL PBS and centrifuged again for 5 min at 700 g at room temperature. The pellet was resuspended in 500uL PBS + 2% FBS and run through a 70uM cell strainer the strainer was then washed with 500uL of PBS + 2% FBS giving a total volume of 1mL. Libraries were prepared for sequencing using Illumina Single Cell 3’ v3.1 Reagents under standard conditions scRNA seq	Embryos were maintained in E3 embryo medium until 52 hpf	treatment:Vegfc MO\|strain:flk:mCherry;cd41:gfp\|age:52 hpf	GSM5655701	GSM5655701: Vegfc MO; Danio rerio; RNA Seq	GSM5655701 r1	GSM5655701	1	Embryos were treated with a dissociation mix consisting of 480 ml 0.25% trypsin EDTA + 20 ml Collagenase 100 mg/ml for 15 mins at 30C. Once embryos were fully homogenized dissociation was stopped with addition of 800 ml of DMEM 10%FBS. The homogenate was run though a 70 uM strainer before centrifugation for 5 min at 700 g at room temperature. The pellet was resuspended in 1mL PBS and centrifuged again for 5 min at 700 g at room temperature. The pellet was resuspended in 500uL PBS + 2% FBS and run through a 70uM cell strainer the strainer was then washed with 500uL of PBS + 2% FBS giving a total volume of 1mL. Libraries were prepared for sequencing using Illumina Single Cell three prime v3.1 Reagents under standard conditions scRNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP343153	VegfcMo_S3_L001_R1_001.fastq.gz VegfcMo_S3_L001_R2_001.fastq.gz	fastq fastq	13667302233.0	116814549.0	GSM5655701 r1	0:28 1:89	A:3845447410;C:3000770206;G:3051184574;T:3769610622;N:289421	28	89	3845447410	3000770206	3051184574	3769610622	289421	SRX12775941	SRS10721245	SRA1317383	Tamplin, Cell and Regenerative Biology, University of Wisconsin-Madison	Tamplin, Cell and Regenerative Biology, University of Wisconsin-Madison	2	0.00828	0.92236	0.00351	0.1852	0.99036	0.75982	0.37956	0.50465	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2021-10-26	Hatching	Embryo	Endothelium	Cardiovascular System
66761	66761	SRR16573984	SRX12775941	SRS10721245	SRP343153	PRJNA774550	Single cell RNA sequencing of zebrafish hematopoietic stem cells and endothelial cells	GSE186565	Transcriptome Analysis	Assessing gene changes in endothelial to hematopoietic transition in control zebrafish embryos and comparing gene changes to those seen in vegfc knock down embryos. Overall design: 52 hpf embryos were dissociated for FACs sorting to isolate GFP+ HSPCs mCherry+ ECs and double positive cells undergoing EHT. Following the sort cells underwent standard 10x encapsulation.		pubmed:34919128	Vegfc MO	GSM5655701	tissue:Endothelial Cells HSPCs\|treatment:Vegfc MO\|strain:flk:mCherry; cd41:gfp\|age:52 hpf	Vegfc MO	Demultiplexing of raw base call files was done using cellranger mkfastq; version 4.0.0 Alignment filtering barcode counting and UMI counting was done using cellranger count; version 4.0.0 Samples were aggregated and normalized using cellranger aggr; version 4.0.0 Genome build: custom GRCz11 reporters Supplementary files format and content: Filtered feature barcode matrix	Endothelial Cells HSPCs	Control samples were not injected uninjected and treated samples were injected with 4 ng of vegfc MO at the one cell stage	Embryos were treated with a dissociation mix consisting of 480 ml 0.25% trypsin EDTA + 20 ml Collagenase 100 mg/ml for 15 mins at 30C. Once embryos were fully homogenized dissociation was stopped with addition of 800 ml of DMEM 10%FBS. The homogenate was run though a 70 uM strainer before centrifugation for 5 min at 700 g at room temperature. The pellet was resuspended in 1mL PBS and centrifuged again for 5 min at 700 g at room temperature. The pellet was resuspended in 500uL PBS + 2% FBS and run through a 70uM cell strainer the strainer was then washed with 500uL of PBS + 2% FBS giving a total volume of 1mL. Libraries were prepared for sequencing using Illumina Single Cell 3’ v3.1 Reagents under standard conditions scRNA seq	Embryos were maintained in E3 embryo medium until 52 hpf	treatment:Vegfc MO\|strain:flk:mCherry;cd41:gfp\|age:52 hpf	GSM5655701	GSM5655701: Vegfc MO; Danio rerio; RNA Seq	GSM5655701 r1	GSM5655701	1	Embryos were treated with a dissociation mix consisting of 480 ml 0.25% trypsin EDTA + 20 ml Collagenase 100 mg/ml for 15 mins at 30C. Once embryos were fully homogenized dissociation was stopped with addition of 800 ml of DMEM 10%FBS. The homogenate was run though a 70 uM strainer before centrifugation for 5 min at 700 g at room temperature. The pellet was resuspended in 1mL PBS and centrifuged again for 5 min at 700 g at room temperature. The pellet was resuspended in 500uL PBS + 2% FBS and run through a 70uM cell strainer the strainer was then washed with 500uL of PBS + 2% FBS giving a total volume of 1mL. Libraries were prepared for sequencing using Illumina Single Cell three prime v3.1 Reagents under standard conditions scRNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP343153	VegfcMo_S3_L002_R1_001.fastq.gz VegfcMo_S3_L002_R2_001.fastq.gz	fastq fastq	13683498777.0	116952981.0	GSM5655701 r2	0:28 1:89	A:3849019312;C:3005132517;G:3056752429;T:3772346961;N:247558	28	89	3849019312	3005132517	3056752429	3772346961	247558	SRX12775941	SRS10721245	SRA1317383	Tamplin, Cell and Regenerative Biology, University of Wisconsin-Madison	Tamplin, Cell and Regenerative Biology, University of Wisconsin-Madison	2	0.00801	0.92192	0.00324	0.18499	0.99099	0.75877	0.37068	0.50141	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2021-10-26	Hatching	Embryo	Endothelium	Cardiovascular System
66762	66762	SRR16573985	SRX12775940	SRS10721244	SRP343153	PRJNA774550	Single cell RNA sequencing of zebrafish hematopoietic stem cells and endothelial cells	GSE186565	Transcriptome Analysis	Assessing gene changes in endothelial to hematopoietic transition in control zebrafish embryos and comparing gene changes to those seen in vegfc knock down embryos. Overall design: 52 hpf embryos were dissociated for FACs sorting to isolate GFP+ HSPCs mCherry+ ECs and double positive cells undergoing EHT. Following the sort cells underwent standard 10x encapsulation.		pubmed:34919128	Uninjected	GSM5655700	tissue:Endothelial Cells HSPCs\|treatment:Uninjected\|strain:flk:mCherry; cd41:gfp\|age:52 hpf	Uninjected	Demultiplexing of raw base call files was done using cellranger mkfastq; version 4.0.0 Alignment filtering barcode counting and UMI counting was done using cellranger count; version 4.0.0 Samples were aggregated and normalized using cellranger aggr; version 4.0.0 Genome build: custom GRCz11 reporters Supplementary files format and content: Filtered feature barcode matrix	Endothelial Cells HSPCs	Control samples were not injected uninjected and treated samples were injected with 4 ng of vegfc MO at the one cell stage	Embryos were treated with a dissociation mix consisting of 480 ml 0.25% trypsin EDTA + 20 ml Collagenase 100 mg/ml for 15 mins at 30C. Once embryos were fully homogenized dissociation was stopped with addition of 800 ml of DMEM 10%FBS. The homogenate was run though a 70 uM strainer before centrifugation for 5 min at 700 g at room temperature. The pellet was resuspended in 1mL PBS and centrifuged again for 5 min at 700 g at room temperature. The pellet was resuspended in 500uL PBS + 2% FBS and run through a 70uM cell strainer the strainer was then washed with 500uL of PBS + 2% FBS giving a total volume of 1mL. Libraries were prepared for sequencing using Illumina Single Cell 3’ v3.1 Reagents under standard conditions scRNA seq	Embryos were maintained in E3 embryo medium until 52 hpf	treatment:Uninjected\|strain:flk:mCherry;cd41:gfp\|age:52 hpf	GSM5655700	GSM5655700: Uninjected; Danio rerio; RNA Seq	GSM5655700 r1	GSM5655700	1	Embryos were treated with a dissociation mix consisting of 480 ml 0.25% trypsin EDTA + 20 ml Collagenase 100 mg/ml for 15 mins at 30C. Once embryos were fully homogenized dissociation was stopped with addition of 800 ml of DMEM 10%FBS. The homogenate was run though a 70 uM strainer before centrifugation for 5 min at 700 g at room temperature. The pellet was resuspended in 1mL PBS and centrifuged again for 5 min at 700 g at room temperature. The pellet was resuspended in 500uL PBS + 2% FBS and run through a 70uM cell strainer the strainer was then washed with 500uL of PBS + 2% FBS giving a total volume of 1mL. Libraries were prepared for sequencing using Illumina Single Cell three prime v3.1 Reagents under standard conditions scRNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP343153	UnInj2_S2_L001_R1_001.fastq.gz UnInj2_S2_L001_R2_001.fastq.gz	fastq fastq	23657101884.0	202197452.0	GSM5655700 r1	0:28 1:89	A:6762677862;C:5216362851;G:5376327033;T:6301229587;N:504551	28	89	6762677862	5216362851	5376327033	6301229587	504551	SRX12775940	SRS10721244	SRA1317383	Tamplin, Cell and Regenerative Biology, University of Wisconsin-Madison	Tamplin, Cell and Regenerative Biology, University of Wisconsin-Madison	2	0.00742	0.92485	0.00268	0.17441	0.99196	0.76497	0.33369	0.53366	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2021-10-26	Hatching	Embryo	Endothelium	Cardiovascular System
66763	66763	SRR16573986	SRX12775940	SRS10721244	SRP343153	PRJNA774550	Single cell RNA sequencing of zebrafish hematopoietic stem cells and endothelial cells	GSE186565	Transcriptome Analysis	Assessing gene changes in endothelial to hematopoietic transition in control zebrafish embryos and comparing gene changes to those seen in vegfc knock down embryos. Overall design: 52 hpf embryos were dissociated for FACs sorting to isolate GFP+ HSPCs mCherry+ ECs and double positive cells undergoing EHT. Following the sort cells underwent standard 10x encapsulation.		pubmed:34919128	Uninjected	GSM5655700	tissue:Endothelial Cells HSPCs\|treatment:Uninjected\|strain:flk:mCherry; cd41:gfp\|age:52 hpf	Uninjected	Demultiplexing of raw base call files was done using cellranger mkfastq; version 4.0.0 Alignment filtering barcode counting and UMI counting was done using cellranger count; version 4.0.0 Samples were aggregated and normalized using cellranger aggr; version 4.0.0 Genome build: custom GRCz11 reporters Supplementary files format and content: Filtered feature barcode matrix	Endothelial Cells HSPCs	Control samples were not injected uninjected and treated samples were injected with 4 ng of vegfc MO at the one cell stage	Embryos were treated with a dissociation mix consisting of 480 ml 0.25% trypsin EDTA + 20 ml Collagenase 100 mg/ml for 15 mins at 30C. Once embryos were fully homogenized dissociation was stopped with addition of 800 ml of DMEM 10%FBS. The homogenate was run though a 70 uM strainer before centrifugation for 5 min at 700 g at room temperature. The pellet was resuspended in 1mL PBS and centrifuged again for 5 min at 700 g at room temperature. The pellet was resuspended in 500uL PBS + 2% FBS and run through a 70uM cell strainer the strainer was then washed with 500uL of PBS + 2% FBS giving a total volume of 1mL. Libraries were prepared for sequencing using Illumina Single Cell 3’ v3.1 Reagents under standard conditions scRNA seq	Embryos were maintained in E3 embryo medium until 52 hpf	treatment:Uninjected\|strain:flk:mCherry;cd41:gfp\|age:52 hpf	GSM5655700	GSM5655700: Uninjected; Danio rerio; RNA Seq	GSM5655700 r1	GSM5655700	1	Embryos were treated with a dissociation mix consisting of 480 ml 0.25% trypsin EDTA + 20 ml Collagenase 100 mg/ml for 15 mins at 30C. Once embryos were fully homogenized dissociation was stopped with addition of 800 ml of DMEM 10%FBS. The homogenate was run though a 70 uM strainer before centrifugation for 5 min at 700 g at room temperature. The pellet was resuspended in 1mL PBS and centrifuged again for 5 min at 700 g at room temperature. The pellet was resuspended in 500uL PBS + 2% FBS and run through a 70uM cell strainer the strainer was then washed with 500uL of PBS + 2% FBS giving a total volume of 1mL. Libraries were prepared for sequencing using Illumina Single Cell three prime v3.1 Reagents under standard conditions scRNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP343153	UnInj2_S2_L002_R1_001.fastq.gz UnInj2_S2_L002_R2_001.fastq.gz	fastq fastq	23583414231.0	201567643.0	GSM5655700 r2	0:28 1:89	A:6738316424;C:5202021444;G:5363779316;T:6278870685;N:426362	28	89	6738316424	5202021444	5363779316	6278870685	426362	SRX12775940	SRS10721244	SRA1317383	Tamplin, Cell and Regenerative Biology, University of Wisconsin-Madison	Tamplin, Cell and Regenerative Biology, University of Wisconsin-Madison	2	0.00772	0.92365	0.0027	0.17244	0.99091	0.76481	0.30847	0.53164	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2021-10-26	Hatching	Embryo	Endothelium	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");;